ArticleNature methods2018
Species-level functional profiling of metagenomes and metatranscriptomes.
Article in Nature methods, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT07169123 (Protease Regulation and Impact of Sodium as Mechanisms of Inflammation in IBD), which is not on this map. Cited by 961 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.
Protease Regulation and Impact of Sodium as Mechanisms of Inflammation in IBD
Who cites it
961 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Marine microbiomes and their expanding role in biotechnological potential: a systematic review.Archives of microbiology · 2026Pooled it
- Worldwide research trends on theFrontiers in immunology · 2026Pooled it
- Akkermansia muciniphila enhances washed microbiota transplantation in the treatment of epilepsy.Chinese medical journal · 2026Trial
- Trial
- Effects of a combined energy restriction and vigorous-intensity exercise intervention on the human gut microbiome: A randomised controlled trial.The Journal of physiology · 2025Trial
- Effects of dietary FODMAP content on the faecal microbiome and gastrointestinal physiology in healthy adults: a randomised, controlled cross-over feeding study.The British journal of nutrition · 2025Trial
- Magnesium treatment increases gut microbiome synthesizing vitamin D and inhibiting colorectal cancer: results from a double-blind precision-based randomized placebo-controlled trial.The American journal of clinical nutrition · 2025Trial
- The Association of Gut Microbiota With TRPM7 Genotype, Colorectal Polyps, and Magnesium.The Journal of nutrition · 2025Trial
- Open-Label, Prospective Study of a Prebiotic Gel Cream on Its Efficacy of Mild to Moderate Acne Management and Effects on the Functional Skin Microbiome.Journal of cosmetic dermatology · 2025Trial
- Changing Gastrointestinal Transit Time Alters Microbiome Composition and Bile Acid Metabolism: A Cross-Over Study in Healthy Volunteers.Neurogastroenterology and motility · 2025Trial
- A Randomized Clinical Trial Evaluating Lactiplantibacillus Plantarum for the Prevention of GI aGvHD: A Report From the Children's Oncology Group (ACCL1633).Transplantation and cellular therapy · 2025Trial
- Gut microbiomes of tribal communities in India vary with dairy and grain consumption.Gut microbes · 2026Article
- Microbiome signatures correlate with diet-mediated ADHD symptom reduction.Gut microbes · 2026Article
- Article
- Bacterial microbiome and flavor metabolome shifts in traditional Hinggan league sauerkraut fermentation.Food chemistry. Molecular sciences · 2026Article
- Gut microbial diversity and candidate keystone taxa in Indian tribes: Insights across lifestyle-ecological continuum and health associations.Current research in microbial sciences · 2026Article
- Microbiome interactions in renal cell carcinoma: evidence, challenges and opportunities.Nature reviews. Urology · 2026Review
- Chestnut-quebracho tannins shape the fecal metabolome of weaned pigs through microbiota-dependent urolithin production.Journal of animal science and biotechnology · 2026Article
- Obesity and Age Elevate Tissue-Resident Microbiota Akkermansia muciniphila to Induce Oxidative Stress and Promote Breast Cancer Risk.Cancer research · 2026Article
- Multi-omics profiling of oral microbial functional signatures and systemic immune-metabolic features in perinatal depression.Brain, behavior, & immunity - health · 2026Article
901 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
11 authors.
Funding
Abstract
Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types.
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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.