ArticlePLoS biology2022
Systematically assessing microbiome-disease associations identifies drivers of inconsistency in metagenomic research.
Article in PLoS biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers, 3 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
22 citing papers in PubMed, 3 syntheses or guidelines pooled it, 46 citations in OpenAlex.
- Meta-analysis of 22,710 human microbiome metagenomes defines an oral-to-gut microbial enrichment score and associations with host health and disease.Nature communications · 2025Pooled it
- A population-scale analysis of 36 gut microbiome studies reveals universal species signatures for common diseases.NPJ biofilms and microbiomes · 2024Pooled it
- Meta-analysis reveals the vaginal microbiome is a better predictor of earlier than later preterm birth.BMC biology · 2023Pooled it
- Brain health and the gut microbiome (bMicrobiome Study): a proof-of-concept, feasibility study integrating shotgun metagenomics, metrology, and multidimensional phenotyping across the cognitive aging spectrum.Gut microbes reports · 2026Article
- Orchestrating the gut microbiota-mitochondrial-immune axis in gynecological diseases: mechanisms and dual-targeting therapeutic strategies.Frontiers in reproductive health · 2026Review
- Specification curve analysis of the TEDDY study reveals large variation in microbiome-based T1D predictive performance.Nature communications · 2025Article
- GIMIC: smoothed graph-image representation of microbiome samples induce an optimal distance.Genome biology · 2025Article
- Non-small Cell Lung Cancer, Immunotherapy and the Influence of Gut Microbiome.Current microbiology · 2025Review
- Restoration of intestinal secondary bile acid synthesis: A potential approach to improve pancreatic β cell function in type 1 diabetes.Cell reports. Medicine · 2025Article
- The role of the gut microbiome in the associations between lead exposure and child neurodevelopment.Toxicology letters · 2025Review
- Longitudinal phage-bacteria dynamics in the early life gut microbiome.Nature microbiology · 2025Article
- Topology of gut Microbiota Network and Guild-Based Analysis in Chinese Adults.Phenomics (Cham, Switzerland) · 2025Article
- Towards geospatially-resolved public-health surveillance via wastewater sequencing.Nature communications · 2024Article
- A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies.Genome biology · 2024Article
- Emergent ecological patterns and modelling of gut microbiomes in health and in disease.PLoS computational biology · 2024Article
- Emergent Functional Organization of Gut Microbiomes in Health and Diseases.Biomolecules · 2023Article
- [The microbiome and metabolic syndrome: is this a chicken-or-egg problem?]Innere Medizin (Heidelberg, Germany) · 2023Review
- Assessment of Energy and Nutrient Intake and the Intestinal Microbiome (ErNst Study): Protocol and Methods of a Cross-sectional Human Observational Study.JMIR research protocols · 2023Article
- Over-optimism in unsupervised microbiome analysis: Insights from network learning and clustering.PLoS computational biology · 2023Article
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Corrections and comments
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Authors and funding
8 authors at 4 institutions in 1 country.
Funding
Abstract
Evaluating the relationship between the human gut microbiome and disease requires computing reliable statistical associations. Here, using millions of different association modeling strategies, we evaluated the consistency-or robustness-of microbiome-based disease indicators for 6 prevalent and well-studied phenotypes (across 15 public cohorts and 2,343 individuals). We were able to discriminate between analytically robust versus nonrobust results. In many cases, different models yielded contradictory associations for the same taxon-disease pairing, some showing positive correlations and others negative. When querying a subset of 581 microbe-disease associations that have been previously reported in the literature, 1 out of 3 taxa demonstrated substantial inconsistency in association sign. Notably, >90% of published findings for type 1 diabetes (T1D) and type 2 diabetes (T2D) were particularly nonrobust in this regard. We additionally quantified how potential confounders-sequencing depth, glucose levels, cholesterol, and body mass index, for example-influenced associations, analyzing how these variables affect the ostensible correlation between Faecalibacterium prausnitzii abundance and a healthy gut. Overall, we propose our approach as a method to maximize confidence when prioritizing findings that emerge from microbiome association studies.
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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 Socratic graph.