ArticleGenome biology2020
Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics applied to microbiome data.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers, 2 of them syntheses that pooled it.
What it found
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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
75 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Fecal Microbial Community Profiling Allows Discrimination of Phenotype and Treatment Response in Pediatric Crohn's Disease and Ulcerative Colitis-An International Meta-Analysis.Inflammatory bowel diseases · 2025Pooled it
- Gut Microbiota in Patients with Polycystic Ovary Syndrome: a Systematic Review.Reproductive sciences (Thousand Oaks, Calif.) · 2022Pooled it
- Resistant dextrin promotes beneficial fecal bacteria in high and low fiber diet populations: a randomized, double-blinded, controlled pilot study.Frontiers in nutrition · 2026Trial
- Gut Microbial Species and Endotypes Associate with Remission in Ulcerative Colitis Patients Treated with Anti-TNF or Anti-integrin Therapy.Journal of Crohn's & colitis · 2024Trial
- L-Glutamine Plus L-Glutamic Acid Enhances Antioxidant Status and Ammonia Toxicity Resilience, Upregulates Interleukin IL-10 Gene, and Improves Gut Microbiota and Survival in Juvenile Nile Tilapia.Journal of animal physiology and animal nutrition · 2026Article
- Changes to Skin Microbiome Community Dynamics Support Resistance to Enzootic and Epizootic Strains of Batrachochytrium dendrobatidis (Bd) in the Spotted Salamander (Ambystoma maculatum).Molecular ecology · 2026Article
- Predator-mediated local convergence fosters global microbial community divergence.Nature communications · 2026Article
- Comprehensive evaluation of statistical approaches for differential metaproteomics.bioRxiv : the preprint server for biology · 2026Article
- Gut Microbiome Differences Across Mixed-Sex and Female-Only Social Rearing Regimes in Female Field CricketsInsects · 2026Article
- Revisiting differential expression analysis: An updated six-dimensional comparative study.PloS one · 2026Article
- Gut Microbiota-Metabolite Alterations Associated with Early Metabolic Dysfunction and Hepatic Steatosis in Adolescents.Computational and structural biotechnology journal · 2026Article
- Oral Microbiome in Oral Cancer Research from Sampling to Analysis: Strategies, Challenges, and Recommendations.Cancers · 2025Review
- Deciphering the personalized functional redundancy hierarchy in the gut microbiome.Microbiome · 2025Article
- "Microbial and immune modulation by 2'-fucosyllactose supplementation during gestation: a strategy to prevent food allergies".Gut microbes · 2025Article
- Exploring the Interplay Between Gut Microbiota and the Melatonergic Pathway in Hormone Receptor-Positive Breast Cancer.International journal of molecular sciences · 2025Article
- Elementary methods provide more replicable results in microbial differential abundance analysis.Briefings in bioinformatics · 2025Article
- PreLect: Prevalence leveraged consistent feature selection decodes microbial signatures across cohorts.NPJ biofilms and microbiomes · 2025Article
- A proposed workflow to robustly analyze bacterial transcripts in RNAseq data from extracellular vesicles.Frontiers in microbiology · 2025Article
- Article
- Wise Roles and Future Visionary Endeavors of Current Emperor: Advancing Dynamic Methods for Longitudinal Microbiome Meta-Omics Data in Personalized and Precision Medicine.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Review
15 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
5 authors.
Funding
Abstract
backgroundThe correct identification of differentially abundant microbial taxa between experimental conditions is a methodological and computational challenge. Recent work has produced methods to deal with the high sparsity and compositionality characteristic of microbiome data, but independent benchmarks comparing these to alternatives developed for RNA-seq data analysis are lacking.
resultsWe compare methods developed for single-cell and bulk RNA-seq, and specifically for microbiome data, in terms of suitability of distributional assumptions, ability to control false discoveries, concordance, power, and correct identification of differentially abundant genera. We benchmark these methods using 100 manually curated datasets from 16S and whole metagenome shotgun sequencing.
conclusionsThe multivariate and compositional methods developed specifically for microbiome analysis did not outperform univariate methods developed for differential expression analysis of RNA-seq data. We recommend a careful exploratory data analysis prior to application of any inferential model and we present a framework to help scientists make an informed choice of analysis methods in a dataset-specific manner.
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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.