ArticleNature methods2012
Metagenomic microbial community profiling using unique clade-specific marker genes.
Article in Nature methods, 2012. 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 1,002 papers, 1 of them a synthesis that pooled it.
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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.
Protease Regulation and Impact of Sodium as Mechanisms of Inflammation in IBD
Who cites it
1,002 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Akkermansia muciniphila enhances washed microbiota transplantation in the treatment of epilepsy.Chinese medical journal · 2026Trial
- The impact of an oral purified microbiome therapeutic on the gastrointestinal microbiome.Nature medicine · 2026Trial
- The Association of Gut Microbiota With TRPM7 Genotype, Colorectal Polyps, and Magnesium.The 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
- Effects of healthy low-carbohydrate diet and time-restricted eating on weight and gut microbiome in adults with overweight or obesity: Feeding RCT.Cell reports. Medicine · 2024Trial
- Resistant starch intake facilitates weight loss in humans by reshaping the gut microbiota.Nature metabolism · 2024Trial
- Modulating a prebiotic food source influences inflammation and immune-regulating gut microbes and metabolites: insights from the BE GONE trial.EBioMedicine · 2023Trial
- MiSurv: an Integrative Web Cloud Platform for User-Friendly Microbiome Data Analysis with Survival Responses.Microbiology spectrum · 2023Trial
- Identifying low-quality features and suboptimal models to enhance phenotype prediction.Patterns (New York, N.Y.) · 2026Article
- SURE-Pipe: a pipeline to compare genomes and extract shared and unique regions.NAR genomics and bioinformatics · 2026Article
- The Role of Gut Microbiota in the Association between Air Pollution and Cognitive Function in Older Adults.Environmental health perspectives · 2026Article
- Optimized Urine Metagenomic Methods Reveal Longitudinal Microbial Community Dynamics and Predictors of Transition from Asymptomatic Colonization to CAUTI.bioRxiv : the preprint server for biology · 2026Article
- The human breast milk microbiome: a landscape review of its composition, origins, and impact on infant health.Archives of microbiology · 2026Review
- Responsible Use of Large Language Models in Microbial Genomics and Bioinformatics: A Life-Science Framework for Reliability, Reproducibility, and Risk-Aware Interpretation.Life (Basel, Switzerland) · 2026Review
- Spatial ecology of theMicrobiology spectrum · 2026Article
- An oral tyrosine challenge test for functional phenotyping of microbiota-derived phenyl sulfate production.npj metabolic health and disease · 2026Article
- Escherichia coli as a gut microbial marker of obesity and its reduction following bariatric treatment.Journal of gastroenterology · 2026Article
942 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
Metagenomic shotgun sequencing data can identify microbes populating a microbial community and their proportions, but existing taxonomic profiling methods are inefficient for increasingly large data sets. We present an approach that uses clade-specific marker genes to unambiguously assign reads to microbial clades more accurately and >50× faster than current approaches. We validated our metagenomic phylogenetic analysis tool, MetaPhlAn, on terabases of short reads and provide the largest metagenomic profiling to date of the human gut. It can be accessed at http://huttenhower.sph.harvard.edu/metaphlan/.
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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.