ArticlemBio2018
Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research.
Article in mBio, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 146 papers, 6 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
146 citing papers in PubMed, 6 syntheses or guidelines pooled it.
- From culture-based to 16S sequencing approaches: oral microbiota changes in aging, frailty, and oral hypofunction - a systematic review.BMC oral health · 2026Pooled it
- Impact of non-standardized reporting on reproducibility, usability, and integration in nasopharyngeal metagenomic research: a systematic review.Frontiers in microbiology · 2026Pooled it
- Multi-cohort ensemble learning framework for vaginal microbiome-based endometrial cancer detection.Frontiers in cellular and infection microbiology · 2025Pooled it
- The gut microbiome-metabolome dataset collection: a curated resource for integrative meta-analysis.NPJ biofilms and microbiomes · 2022Pooled it
- Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin.Genome biology · 2022Pooled it
- A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations.Microbiome · 2021Pooled it
- The Gut Microbiota-Epilepsy Axis: Bibliometric Trends, Mechanistic Insights, and Microbiota-Targeted Next-Generation Therapeutic Opportunities.Molecular neurobiology · 2026Review
- Integrative multicohort analysis reveals consistent sex differences in gut microbiota of multiple sclerosis patients.mSystems · 2026Article
- Multidisciplinary Delphi consensus statement on minimal standards for clinical metadata and end points in microbiome studies.Nature reviews. Gastroenterology & hepatology · 2026Review
- Pipettes and Pipelines: The Weapons of Omics Sciences for a New Age of Clinical Studies.Current issues in molecular biology · 2026Review
- Translational human gut microbiome research: What are the missing pieces of the puzzle?Journal of translational medicine · 2026Review
- From diet to function: using synthetic microbial communities to map gut microbial interactions.NPJ biofilms and microbiomes · 2026Review
- Microbiota variation inMicrobiology spectrum · 2026Article
- The cancer-microbiome axis: Mechanisms and emerging therapeutic strategies.Seminars in immunopathology · 2026Review
- Eco-tank Housing Maintains Wild-Type Microbiota and Rewilds the Laboratory Mouse Gut Microbiome to Restore Natural Immune Tone.bioRxiv : the preprint server for biology · 2026Article
- Comparison of Spatio-Temporal Dynamics and Composition in Size-Fractionated and Unfractionated Northwestern Atlantic Microbial Communities.Environmental microbiology reports · 2026Article
- EasyMultiProfiler: an efficient multi-omics data integration and analysis workflow for microbiome research.Science China. Life sciences · 2026Article
- Causal Effects of Gut Microbiota and Associated Metabolites on Retinal Diseases and Visual Impairment: A Mendelian Randomization Study.Journal of ophthalmology · 2026Article
- The limit of detection of amicroPublication biology · 2026Article
- FAVABEAN and FALAPhyl: Open-source pipelines for scalable 16s rRNA microbiome data processing and visualization.PloS one · 2026Article
86 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
1 author.
Funding
Abstract
The "reproducibility crisis" in science affects microbiology as much as any other area of inquiry, and microbiologists have long struggled to make their research reproducible. We need to respect that ensuring that our methods and results are sufficiently transparent is difficult. This difficulty is compounded in interdisciplinary fields such as microbiome research. There are many reasons why a researcher is unable to reproduce a previous result, and even if a result is reproducible, it may not be correct. Furthermore, failures to reproduce previous results have much to teach us about the scientific process and microbial life itself. This Perspective delineates a framework for identifying and overcoming threats to reproducibility, replicability, robustness, and generalizability of microbiome research. Instead of seeing signs of a crisis in others' work, we need to appreciate the technical and social difficulties that limit reproducibility in the work of others as well as our own.
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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.