ArticleeLife2019
Consistent and correctable bias in metagenomic sequencing experiments.
Article in eLife, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 237 papers, 4 of them syntheses 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
237 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Metagenomics or Metataxonomics: Best Practice Methods to Uncover the Sinus Microbiome.International forum of allergy & rhinology · 2025Guideline
- Melody: meta-analysis of microbiome association studies for discovering generalizable microbial signatures.Genome biology · 2025Pooled it
- Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases.mSystems · 2024Pooled it
- Meta-analysis reveals the vaginal microbiome is a better predictor of earlier than later preterm birth.BMC biology · 2023Pooled it
- An Interpretable Machine Learning Approach to Ecologically Characterize Soil Carbon and Structure From Multi-Kingdom Microbiome, Texture and Climate.Molecular ecology · 2026Article
- Gut Microbiomes of Two Bamboo Locusts Reveal Divergent Metabolic Potentials.Ecology and evolution · 2026Article
- Robust and Interpretable Metagenomic Modeling Through Structure-Aware Multi-View Learning and Attribution-Guided Biological Insight.Research square · 2026Article
- Microbiome and aging: Trajectories of microbiome age across human ecosystems and their systemic effects.iMeta · 2026Review
- A damage-aware NGS workflow for conservative species identification from ultra-degraded DNA.Analytical and bioanalytical chemistry · 2026Article
- Spatially resolved fetal and maternal cell contributions to severe preeclampsia across gestation.Science advances · 2026Article
- Deterministic selection and compositional turnover in Parkinson's disease-associated gut dysbiosis.Antonie van Leeuwenhoek · 2026Article
- mBatchNet: an interactive web server for diagnosis, correction, and benchmarking of batch effects in microbiome data.Bioinformatics (Oxford, England) · 2026Article
- International Airport Wastewater as a Sentinel Site for Genomic Surveillance of Human Viruses and Bacteriophages.Microorganisms · 2026Article
- Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.Scientific reports · 2026Article
- TestNet: a method for inferring microbial networks with false discovery rate control for clustered and unclustered samples.Genome biology · 2026Article
- Meta-analytic microbiome target discovery for immune checkpoint inhibitor response in advanced melanoma.Communications medicine · 2026Article
- Comprehensive cross-cohort analysis reveals global gut microbiome signatures of celiac disease.Communications medicine · 2026Article
- Cooperative traits maintain bacterial niche breadth.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Fast and reliable association discovery in large-scale microbiome studies and meta-analyses using PALM.bioRxiv : the preprint server for biology · 2026Article
- MaAsLin 3: refining and extending generalized multivariable linear models for meta-omic association discovery.Nature methods · 2026Article
177 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
Marker-gene and metagenomic sequencing have profoundly expanded our ability to measure biological communities. But the measurements they provide differ from the truth, often dramatically, because these experiments are biased toward detecting some taxa over others. This experimental bias makes the taxon or gene abundances measured by different protocols quantitatively incomparable and can lead to spurious biological conclusions. We propose a mathematical model for how bias distorts community measurements based on the properties of real experiments. We validate this model with 16S rRNA gene and shotgun metagenomics data from defined bacterial communities. Our model better fits the experimental data despite being simpler than previous models. We illustrate how our model can be used to evaluate protocols, to understand the effect of bias on downstream statistical analyses, and to measure and correct bias given suitable calibration controls. These results illuminate new avenues toward truly quantitative and reproducible metagenomics measurements.
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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.