ArticleeLife2021
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3.
Article in eLife, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to 3 registered trials, which are not on this map. Cited by 1,509 papers.
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.
A Non-invasive Gut Microbiome-based Diagnostic Tool for the Screening of Colorectal Cancer
A Gut Microbiome-based Diagnostic Tool for the Screening of Colorectal Cancer
Disentangling Microbiome Engraftment by Multi-omics of the Gut Ecosystem During Fecal Transplant
Who cites it
1,509 citing papers in PubMed.
- Synbiotic supplementation leads to gut microbiome communities with functional capacity linked to better brain white matter development in preterm infants.Gut microbes · 2026Trial
- The Safety, Efficacy, and Feasibility of Fecal Microbiota Transplantation in a Population With Bipolar Disorder During Depressive Episodes: A Pilot Parallel Arm Randomized Controlled Trial: Sécurité, efficacité et faisabilité de la transplantation de microbiote fécal chez une population atteinte de troubles bipolaires, au cours d'épisodes dépressifs : essai pilote contrôlé à répartition aléatoire et à groupes parallèles.Canadian journal of psychiatry. Revue canadienne de psychiatrie · 2026Trial
- Resistant starch types 2 and 4 induce distinct and reversible changes in the human gut microbiome.Microbiology spectrum · 2026Trial
- Clinical Trial: Multi-Strain Probiotic Improves Bile Acid Profile, Microbiome, and Metabolomic Parameters in Patients With History of Bile Acid Malabsorption-A Randomized, Controlled Trial.Alimentary pharmacology & therapeutics · 2026Trial
- Dynamics of tumor ecosystems and microbiome in response to neoadjuvant ABFOLFOX treatment in patients with unresectable colorectal cancer with liver metastasis.Genome medicine · 2026Trial
- Combined high-quality metagenomics reveals off-target effects of albendazole, ivermectin-albendazole and moxidectin-albendazole on the human gut bacteria.NPJ biofilms and microbiomes · 2026Trial
- Effect of Household Air Pollution on the Gut Microbiome and Virome of Adult Women Living in Uganda.Environmental health perspectives · 2026Trial
- Testosterone administration partially modulates gut microbiota responses to severe energy deficit.American journal of physiology. Endocrinology and metabolism · 2026Trial
- Effects of Soluble Corn Fiber Consumption on Executive Functions and Gut Microbiota in Middle to Older Age Adults: A Randomized Controlled Crossover Trial.The Journal of nutrition · 2026Trial
- Faecalibacterium prausnitzii EXL01 for the Maintenance of Steroid-induced Clinical Response or Remission in Patients with Crohn's Disease: a first in human trial.Nature communications · 2026Trial
- Alcohol consumption and colorectal carcinogenesis: an exploration of the gut microbial pathway as a potential mediator.European journal of nutrition · 2026Trial
- Impact of Yogurt and Rolled Oats Consumption on the Gut Microbiome: A Randomized Crossover Study Displaying Individual Responses and General Resilience.The Journal of nutrition · 2026Trial
- LGTM: Gaussian process modulated neural topic modeling for longitudinal microbiome.Gut microbes · 2026Article
- Article
- metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.Gut microbes · 2026Article
- GutMIND: A multi-cohort machine learning framework for integrative characteristics of the microbiota-gut-brain axis in neuropsychiatric disorders.Gut microbes · 2026Article
- High dietary BGut microbes · 2026Article
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- Longitudinal gut microbiome dynamics are associated with clinical outcome and toxicity during ibrutinib therapy.Gut microbes · 2026Article
1,449 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
17 authors.
Funding
Abstract
Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and IBD (1635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unraveled the phylogenetic and functional structure of the common gut microbe
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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.