ArticleNature communications2021
An extended reconstruction of human gut microbiota metabolism of dietary compounds.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Revealing interactions between microbes, metabolites, and dietary compounds using genome-scale analysis.Microbiome · 2026Article
- RetroRules 2026: an expanded database combining biochemical and organic reaction templates for pathway discovery.Nucleic acids research · 2026Article
- Modulatory effects of Boletus edulis on the gut microbiota in Atlantic salmon (Salmo salar) utilizing an artificial teleost gut model.Animal microbiome · 2025Article
- Fat-rich diet promotes microbiome-dependent ATP synthesis in sheep model.Journal of animal science and biotechnology · 2025Article
- Chemical Complexity of Food and Implications for Therapeutics.The New England journal of medicine · 2025Review
- Recent advances in precision nutrition and cardiometabolic diseases.Revista espanola de cardiologia (English ed.) · 2025Review
- Dietary patterns influencing the human colonic microbiota from infancy to centenarian age: a narrative review.Frontiers in nutrition · 2025Review
- Gut-Bone Axis Mediates Exercise Modality-Dependent Suppression of Inflammatory Osteoclastogenesis in Ovariectomy-Induced Bone Loss.Mediators of inflammation · 2025Article
- Article
- q2-metnet: QIIME2 package to analyse 16S rRNA data via high-quality metabolic reconstructions of the human gut microbiota.Bioinformatics (Oxford, England) · 2024Article
- Gut microbiota drives colon cancer risk associated with diet: a comparative analysis of meat-based and pesco-vegetarian diets.Microbiome · 2024Article
- Decoding the Foodome: Molecular Networks Connecting Diet and Health.Annual review of nutrition · 2024Review
- Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota.NPJ systems biology and applications · 2024Article
- Engineering Gut Symbionts: A Way to Promote Bee Growth?Insects · 2024Review
- BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities.Bioinformatics (Oxford, England) · 2024Article
- Flux sampling in genome-scale metabolic modeling of microbial communities.BMC bioinformatics · 2024Article
- Therapeutic applications of gut microbes in cardiometabolic diseases: current state and perspectives.Applied microbiology and biotechnology · 2024Review
- Flux Sampling in Genome-scale Metabolic Modeling of Microbial Communities.bioRxiv : the preprint server for biology · 2023Article
- Towards applications of genome-scale metabolic model-based approaches in designing synthetic microbial communities.Quantitative biology (Beijing, China) · 2023Review
- Role of gut microbiota metabolism and biotransformation on dietary natural products to human health implications with special reference to biochemoinformatics approach.Journal of traditional and complementary medicine · 2023Review
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding how diet and gut microbiota interact in the context of human health is a key question in personalized nutrition. Genome-scale metabolic networks and constraint-based modeling approaches are promising to systematically address this complex problem. However, when applied to nutritional questions, a major issue in existing reconstructions is the limited information about compounds in the diet that are metabolized by the gut microbiota. Here, we present AGREDA, an extended reconstruction of diet metabolism in the human gut microbiota. AGREDA adds the degradation pathways of 209 compounds present in the human diet, mainly phenolic compounds, a family of metabolites highly relevant for human health and nutrition. We show that AGREDA outperforms existing reconstructions in predicting diet-specific output metabolites from the gut microbiota. Using 16S rRNA gene sequencing data of faecal samples from Spanish children representing different clinical conditions, we illustrate the potential of AGREDA to establish relevant metabolic interactions between diet and gut microbiota.
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