ArticleNucleic acids research2023
MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 353 papers, 1 of them a synthesis that pooled it.
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Who cites it
353 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Transforming evidence synthesis: A systematic review of the evolution of automated meta-analysis in the age of AI.Research synthesis methods · 2026Pooled 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
- Trial
- 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
- Gut microbiome drives glycodeoxycholic acid-mediated attenuation of hypertension.Gut microbes · 2026Article
- Dietary tryptophan mitigates lung ischemia-reperfusion injury in association with increased indole-3-propionate and aryl hydrocarbon receptor signaling.Gut microbes · 2026Article
- Supplementation withThe veterinary quarterly · 2026Article
- A systematic assessment of the short- and long-term effects of commonly used breast cancer chemotherapeutics on the gut microbiome‒blood‒brain axis of female mice.Gut microbes · 2026Article
- Article
- The core taxa connectivity in leaf microbiomes in ash trees stands is modulated by host-related and environmental factors.Environmental microbiome · 2026Article
- Exploratory integrative analysis of infant gut microbiome and metabolome suggests diet- and microbiome-derived metabolites associated with childhood asthma.Metabolomics : Official journal of the Metabolomic Society · 2026Article
- Integrated Multi-Omics Reveals Complementary Luminal and Mucosal Host-Microbiome Interactions Associated with Disease Activity and Phenotype in Paediatric Inflammatory Bowel Disease.Microorganisms · 2026Article
- Article
- The Biotechnological Applications of Marine Bacteria.Biology · 2026Review
- Tumor Topography Remodels TME Signalling via Compartment-Specific Host-Microbiome-Tumor Crosstalk in Hepatoblastoma.Cancers · 2026Article
- Early-Life Dietary Protein Source Reshapes Gut Microbiota but Fails to Curtail Diet-Induced Metabolic Syndrome in Young Rats.Obesity (Silver Spring, Md.) · 2026Article
- Article
- Microbiome analysis and epigenetic patterns revealed distinct differences between two elm species with contrasting Dutch elm disease resistance.Microbiome · 2026Article
- Using MetaboAnalyst 6.0 for exposomics data analysis-from LC-MS2 spectra processing to dose-response modeling and causal inference.Nature protocols · 2026Review
- Single-cell detection and quantification of the microbiota by MicFLY.Cell host & microbe · 2026Article
293 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbiome studies have become routine in biomedical, agricultural and environmental sciences with diverse aims, including diversity profiling, functional characterization, and translational applications. The resulting complex, often multi-omics datasets demand powerful, yet user-friendly bioinformatics tools to reveal key patterns, important biomarkers, and potential activities. Here we introduce MicrobiomeAnalyst 2.0 to support comprehensive statistics, visualization, functional interpretation, and integrative analysis of data outputs commonly generated from microbiome studies. Compared to the previous version, MicrobiomeAnalyst 2.0 features three new modules: (i) a Raw Data Processing module for amplicon data processing and taxonomy annotation that connects directly with the Marker Data Profiling module for downstream statistical analysis; (ii) a Microbiome Metabolomics Profiling module to help dissect associations between community compositions and metabolic activities through joint analysis of paired microbiome and metabolomics datasets; and (iii) a Statistical Meta-Analysis module to help identify consistent signatures by integrating datasets across multiple studies. Other important improvements include added support for multi-factor differential analysis and interactive visualizations for popular graphical outputs, updated methods for functional prediction and correlation analysis, and expanded taxon set libraries based on the latest literature. These new features are demonstrated using a multi-omics dataset from a recent type 1 diabetes study. MicrobiomeAnalyst 2.0 is freely available at microbiomeanalyst.ca.
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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.