ArticleNature protocols2020
Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data.
Article in Nature protocols, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 855 papers, 2 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
855 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Exploring the chicken respiratory microbiome: a comprehensive meta-analysis of factors shaping chicken respiratory microbiota.Scientific reports · 2026Pooled it
- Engrafting gut bacteriophages have potential to modulate microbial metabolism in fecal microbiota transplantation.Microbiome · 2025Pooled it
- A prospective randomized controlled pilot study of gut microbiome modulation by Nigella sativa seed oil and thymoquinone metabolism in healthy volunteers: implications for gastrointestinal surgery.Scientific reports · 2026Trial
- Signatures in the gut microbiome of German elite athletes: insights from a matched-subgroup analysis.mSystems · 2026Trial
- Oral microbiome modulation mitigates hyperglycemia exacerbation in gestational diabetes mellitus.Nature communications · 2026Trial
- Nutritional Stunting Is Linked to Reduced Oral Microbiome Stability and Reconfigured Microbial Networks in Children: A Pilot Intervention Study.Pathogens (Basel, Switzerland) · 2026Trial
- Gut microbial community and host intestinal gene expression with combined fish oil and soluble corn fiber compared with corn oil and maltodextrin: A randomized crossover trial in healthy older individuals.The American journal of clinical nutrition · 2025Trial
- Evolution in the Peri-Implant Oral Microbiome and Their Relationship to Long-Term Marginal Bone Loss: A Randomized Clinical Study.Clinical oral implants research · 2025Trial
- Effects of phototherapy combined with Lactobacillus salivarius AP-32 or Bifidobacterium animalis subsp. lactis CP-9 on improving neonatal jaundice and gut microbiome health: a randomized double-blind clinical study.Nutrition journal · 2025Trial
- Impact of Probiotic Formula (Lacto-5X) on Constipation: Improvements in Gastrointestinal Symptoms, Gut Microbiome, and Metabolites.Journal of microbiology and biotechnology · 2025Trial
- Effects of combined prebiotic fiber supplementation and weight loss counseling in adults with metabolic dysfunction-associated steatotic liver disease: a randomized controlled trial.European journal of nutrition · 2025Trial
- Effects of Supplementation with Microalgae Extract fromNutrients · 2025Trial
- Trial
- Targeting the microbiome in pediatric migraine: gastrointestinal manifestations and the therapeutic role ofGut microbes · 2026Article
- Human fecal transplantation from stunted children promotes metabolic dysfunction in mice fed with a high-fat and high-fructose corn syrup diet.Gut microbes · 2026Article
- Article
- Dietary tryptophan mitigates lung ischemia-reperfusion injury in association with increased indole-3-propionate and aryl hydrocarbon receptor signaling.Gut microbes · 2026Article
- Postbiotics enhance immune competence in black rockfish (Sebastes schlegelii): linking innate immunity, apoptosis, and resistance to bacterial infection.Journal of animal science and biotechnology · 2026Article
- Dual legacy of plant water-deficit-tolerance and watering history shapes rhizosphere microbial transplant outcomes in tomato post-drought recovery.Environmental microbiome · 2026Article
- Bacterial metagenomic analysis of patients with chronic kidney disease undergoing hemodialysis based on 16S rDNA amplicon sequencing.Biomedical reports · 2026Article
795 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
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MicrobiomeAnalyst is an easy-to-use, web-based platform for comprehensive analysis of common data outputs generated from current microbiome studies. It enables researchers and clinicians with little or no bioinformatics training to explore a wide variety of well-established methods for microbiome data processing, statistical analysis, functional profiling and comparison with public datasets or known microbial signatures. MicrobiomeAnalyst currently contains four modules: Marker-gene Data Profiling (MDP), Shotgun Data Profiling (SDP), Projection with Public Data (PPD), and Taxon Set Enrichment Analysis (TSEA). This protocol will first introduce the MDP module by providing a step-wise description of how to prepare, process and normalize data; perform community profiling; identify important features; and conduct correlation and classification analysis. We will then demonstrate how to perform predictive functional profiling and introduce several unique features of the SDP module for functional analysis. The last two sections will describe the key steps involved in using the PPD and TSEA modules for meta-analysis and visual exploration of the results. In summary, MicrobiomeAnalyst offers a one-stop shop that enables microbiome researchers to thoroughly explore their preprocessed microbiome data via intuitive web interfaces. The complete protocol can be executed in ~70 min.
Indexed as
Identifiers
31942082What 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.