ArticleCurrent protocols in bioinformatics2020
QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data.
Article in Current protocols in bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 279 papers, 2 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
279 citing papers in PubMed, 2 syntheses or guidelines pooled it, 536 citations in OpenAlex.
- The impact of tuberculosis and its treatment on the lung and gut microbiota: a global systematic review, meta-analysis, and amplicon-based metagenomic meta-analysis.BMC infectious diseases · 2025Pooled it
- Human microbiota dysbiosis after SARS-CoV-2 infection have the potential to predict disease prognosis.BMC infectious diseases · 2023Pooled it
- A Randomized Controlled Crossover Lifestyle Intervention to Improve Metabolic and Mental Health in Female Healthcare Night-Shift Workers.Nutrients · 2025Trial
- Integrative multi-omics analysis uncovers tumor-immune-gut axis influencing immunotherapy outcomes in ovarian cancer.Nature communications · 2024Trial
- An open label, non-randomized study assessing a prebiotic fiber intervention in a small cohort of Parkinson's disease participants.Nature communications · 2023Trial
- Host genetic variation is associated with root-associated microbiome assembly and resistance to Fusarium oxysporum in tobacco.Plant physiology · 2026Article
- Predicted shifts in microbial functional potential across the late glacial to holocene transition: a 16S rRNA-based inference from southeastern Arabian Sea sediments.Antonie van Leeuwenhoek · 2026Article
- Insights into the dynamics of antibiotic resistance genes in the human gut microbiome across populations.Gut pathogens · 2026Article
- DietaryAnimals : an open access journal from MDPI · 2026Article
- Microbes Drive Straw Decomposition and Microbial Metabolism in Mollisols with Different Straw Return Rates.Microorganisms · 2026Article
- Effect of Protein Supplementation on the Gut Microbiome of Omnivorous and Herbivorous Goliath Beetles.Insects · 2026Article
- Marine antifouling biocide 4,5-dichloro-2-n-octyl-4-isothiazolin-3-one disrupts sediment microbiome structure and function: insights from absolute quantification and enzyme activity dynamics.Applied and environmental microbiology · 2026Article
- Phase I Evaluation of Patients with Newly Diagnosed Glioblastoma Treated with Radiation, Nivolumab, and IDO1 Enzyme Inhibitor BMS-986205.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- PasteurizedMicrobiology spectrum · 2026Article
- Effects of Timing of Microbial Exposure on Microbiome Assembly and Amphibian Immune Development.Ecology and evolution · 2026Article
- Host Mucosal Niche and Rearing Environment Are Associated with Distinct Gut and Gill Microbiota ofVeterinary sciences · 2026Article
- Maternal Metformin Exposure Induces Gut Microbial Shifts in Non-Diabetic Dams and Sex-Stratified Changes in Mouse Offspring.Biomolecules · 2026Article
- A Novel Blend ofFoods (Basel, Switzerland) · 2026Article
- Discovery of specific rhizosphere bacteriaScience advances · 2026Article
- Comparing Asymptomatic Versus Symptomatic Bacterial Vaginosis: Clinical Characteristics, Vaginal Microbiota, and Lactic Acid Profiles.Sexually transmitted diseases · 2026Article
219 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
14 authors at 3 institutions in 2 countries.
Funding
Abstract
QIIME 2 is a completely re-engineered microbiome bioinformatics platform based on the popular QIIME platform, which it has replaced. QIIME 2 facilitates comprehensive and fully reproducible microbiome data science, improving accessibility to diverse users by adding multiple user interfaces. QIIME 2 can be combined with Qiita, an open-source web-based platform, to re-use available data for meta-analysis. The following basic protocol describes how to install QIIME 2 on a single computer and analyze microbiome sequence data, from processing of raw DNA sequence reads through generating publishable interactive figures. These interactive figures allow readers of a study to interact with data with the same ease as its authors, advancing microbiome science transparency and reproducibility. We also show how plug-ins developed by the community to add analysis capabilities can be installed and used with QIIME 2, enhancing various aspects of microbiome analyses-e.g., improving taxonomic classification accuracy. Finally, we illustrate how users can perform meta-analyses combining different datasets using readily available public data through Qiita. In this tutorial, we analyze a subset of the Early Childhood Antibiotics and the Microbiome (ECAM) study, which tracked the microbiome composition and development of 43 infants in the United States from birth to 2 years of age, identifying microbiome associations with antibiotic exposure, delivery mode, and diet. For more information about QIIME 2, see https://qiime2.org. To troubleshoot or ask questions about QIIME 2 and microbiome analysis, join the active community at https://forum.qiime2.org. © 2020 The Authors. Basic Protocol: Using QIIME 2 with microbiome data Support Protocol: Further microbiome analyses.
Indexed as
Identifiers
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.