ArticleNature metabolism2025
Metagenomic estimation of dietary intake from human stool.
Article in Nature metabolism, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 27 papers.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed.
- From gut dysbiosis to eubiosis: understanding microbiome recovery as an ecological process.Gut microbes · 2026Review
- [Research progress of metabolomics in the pathogenesis and treatment of constipation in children].Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics · 2026Review
- Sequencing what we eat.Nature reviews. Gastroenterology & hepatology · 2026Article
- FoodScribe: an open-source semantic framework for nutrient estimation from free-text dietary records.medRxiv : the preprint server for health sciences · 2026Article
- Advances and opportunities in measuring dietary intake: from omics to AI.Nature metabolism · 2026Review
- Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum.Microbiome · 2026Article
- Soy and the gut microbiome: a bi-directional relationship shaping nutrition and health.European journal of nutrition · 2026Review
- The food matrix as a confounder in diet‒microbiome studies: methodological challenges and research gaps.Gut microbes reports · 2026Review
- Wastewater metaproteomics: tracking microbial and human protein biomarkers.ISME communications · 2026Article
- Integration of modern technologies to advance dietary assessment.Nature food · 2026Review
- Genomics of host-microbiome interactions in humans.Nature reviews. Genetics · 2026Review
- Precision nutrition through diet-gut microbiome interactions: Emerging insights driven by artificial intelligence, microbiome health metrics, and mechanistic modeling.Gut microbes reports · 2026Review
- Capturing static and dynamic dietary patterns for human gut microbiome research: a conceptual framework.Gut microbes reports · 2026Review
- Human biomonitoring of mycotoxins: key challenges and future directions.Mycotoxin research · 2025Review
- Shifts in the human gut microbiome during cancer chemotherapy are diet-dependent.bioRxiv : the preprint server for biology · 2025Article
- Decay of Food DNA in the Gastrointestinal Tract: Implications for Molecular Dietary Records.Nutrients · 2025Article
- Faecal metabolites as a readout of habitual diet capture dietary interactions with the gut microbiome.Nature communications · 2025Article
- Multidomain therapy for Alzheimer's disease: a scoping review of cognitive decline trials.Molecular neurodegeneration · 2025Article
- Learning molecular fingerprints of foods to decode dietary intake.Research square · 2025Article
- Targeting the Gut Microbiota's Role in Host Energy Absorption With Precision Nutrition Interventions for the Prevention and Treatment of Obesity.Nutrition reviews · 2025Review
Corrections and comments
- Erratum issued
- Update of
Authors and funding
6 authors.
Funding
Abstract
Dietary intake is tightly coupled to gut microbiota composition, human metabolism and the incidence of virtually all major chronic diseases. Dietary and nutrient intake are usually assessed using self-reporting methods, including dietary questionnaires and food records, which suffer from reporting biases and require strong compliance from study participants. Here, we present Metagenomic Estimation of Dietary Intake (MEDI): a method for quantifying food-derived DNA in human faecal metagenomes. We show that DNA-containing food components can be reliably detected in stool-derived metagenomic data, even when present at low abundances (more than ten reads). We show how MEDI dietary intake profiles can be converted into detailed metabolic representations of nutrient intake. MEDI identifies the onset of solid food consumption in infants, shows significant agreement with food frequency questionnaire responses in an adult population and shows agreement with food and nutrient intake in two controlled-feeding studies. Finally, we identify specific dietary features associated with metabolic syndrome in a large clinical cohort without dietary records, providing a proof-of-concept for detailed tracking of individual-specific, health-relevant dietary patterns without the need for questionnaires.
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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.