ArticleProtein & cell2023
The best practice for microbiome analysis using R.
Article in Protein & cell, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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
70 citing papers in PubMed.
- Modulating effects of microbiota on synbiotic intervention outcomes for microbiota-derived trimethylamine, trimethylamine N-oxide and indoxyl sulfate in healthy young medical students: insights from a 12-week randomized clinical trial.Journal of translational medicine · 2025Trial
- Latent tuberculosis infection shapes gut microbiome and immune-metabolic interactions in people living with HIV.Gut microbes · 2026Article
- Article
- Stimulating the non-ARG harbored microbes with a specific carbon source can suppress the rebound of soil ARB after calcium peroxide application.Fundamental research · 2026Article
- Review
- Article
- Tracking Gut Homeostasis: Key Taxa Transitions and Core Network Hyper-Connectivity as Early Signals of Dysbiosis.Biomedicines · 2026Article
- Dimethylsulfoniopropionate metabolism shapes microbial ecology and physiological adaptation during the austral winter in Southern Ocean sea ice and seawater.Nature communications · 2026Article
- Article
- Community Succession and Diversity Variation of Endophytic and Rhizosphere Soil Bacteria AcrossBiology · 2026Article
- DietaryAntibiotics (Basel, Switzerland) · 2026Article
- A workflow for statistical analysis and visualization of microbiome omics data using the R microeco package.Nature protocols · 2026Review
- Phosphorus availability drives rhizosphere metabolite-microbial community interactions to modulate cucumber susceptibility to Fusarium wilt.Microbiome · 2026Article
- Why Clinical Trials of Microbiome-Targeted Interventions Often Fail to Support Health Claims: A Commentary on Probiotics and Translational Design.Microorganisms · 2026Article
- Feeding Type Shapes Infant Gut Microbiota and Metabolite Profiles in a Simulated Colonic Model.Microorganisms · 2026Article
- Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing.Microorganisms · 2026Review
- Deciphering the keystone position of abundant species within surface-dwelling microbial aggregates in paddy soils.Applied and environmental microbiology · 2026Article
- Article
- Cross-cohort resistome and virulome gradients structure the colorectal cancer microbiome.NPJ biofilms and microbiomes · 2026Article
- Gut fungi exacerbates gallstone formation by activating neutrophil extracellular traps in the liver.Apoptosis : an international journal on programmed cell death · 2026Article
10 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
6 authors.
Funding
Abstract
With the gradual maturity of sequencing technology, many microbiome studies have published, driving the emergence and advance of related analysis tools. R language is the widely used platform for microbiome data analysis for powerful functions. However, tens of thousands of R packages and numerous similar analysis tools have brought major challenges for many researchers to explore microbiome data. How to choose suitable, efficient, convenient, and easy-to-learn tools from the numerous R packages has become a problem for many microbiome researchers. We have organized 324 common R packages for microbiome analysis and classified them according to application categories (diversity, difference, biomarker, correlation and network, functional prediction, and others), which could help researchers quickly find relevant R packages for microbiome analysis. Furthermore, we systematically sorted the integrated R packages (phyloseq, microbiome, MicrobiomeAnalystR, Animalcules, microeco, and amplicon) for microbiome analysis, and summarized the advantages and limitations, which will help researchers choose the appropriate tools. Finally, we thoroughly reviewed the R packages for microbiome analysis, summarized most of the common analysis content in the microbiome, and formed the most suitable pipeline for microbiome analysis. This paper is accompanied by hundreds of examples with 10,000 lines codes in GitHub, which can help beginners to learn, also help analysts compare and test different tools. This paper systematically sorts the application of R in microbiome, providing an important theoretical basis and practical reference for the development of better microbiome tools in the future. All the code is available at GitHub github.com/taowenmicro/EasyMicrobiomeR.
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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.