ArticleGut microbes
Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut.
Article in Gut microbes. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 127 papers, 1 of them a synthesis that pooled it.
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Who cites it
127 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Systematic review of the effects of the intestinal microbiota on selected nutrients and non-nutrients.European journal of nutrition · 2018Pooled it
- Fecal microbiome and metabolome of infants fed bovine MFGM supplemented formula or standard formula with breast-fed infants as reference: a randomized controlled trial.Scientific reports · 2019Trial
- Personalized whole-body modeling links gut microbiota to metabolic perturbations in Alzheimer's disease.Gut microbes · 2026Article
- Genome-scale metabolic models predict diet- and lifestyle-driven shifts of ecological interactions in the gut microbiome.Gut microbes · 2026Article
- Separating extracellular from intracellular fecal metabolites exposes cross-feeding architecture in the gut: exploring metabolite partitioning and ecological associations.Gut microbes · 2026Article
- Heterotrophic feeding and symbiotic state shape the chemical microenvironment, microbiome composition, and activity in the coral gastrovascular cavity.Applied and environmental microbiology · 2026Article
- Integrating host-microbiome multi-omics with machine learning: methods, benchmarks, and translational applications.Science China. Life sciences · 2026Review
- Rational engineering of facultative anaerobiosis enables commensal survival in the oxygenated gut.bioRxiv : the preprint server for biology · 2026Article
- ModellingCurrent research in microbial sciences · 2026Article
- Ecology of the gut microbiota and colonization resistance: mechanisms and therapeutic implications.FEMS microbiology ecology · 2025Review
- Prediabetes and type 2 diabetes but not obesity are associated with alterations in bile acid related gut microbe-microbe and gut microbe-host community metabolism.Gut microbes · 2025Article
- Metabolic modeling links gut microbiota to metabolic markers of Parkinson's disease.Gut microbes · 2025Article
- Genome-scale metabolic model-guided systematic framework for designing customized live biotherapeutic products.NPJ systems biology and applications · 2025Review
- Reducing redundancy and enhancing accuracy through a phylogenetically-informed microbial community metabolic modeling approach.Bioinformatics (Oxford, England) · 2025Article
- Genome-scale metabolic modeling reveals specific vaginalMicrobiology spectrum · 2025Article
- Metabolic modeling reveals a multi-level deregulation of host-microbiome metabolic networks in IBD.Nature communications · 2025Article
- Metabolic modelling reveals increased autonomy and antagonism in type 2 diabetic gut microbiota.Molecular systems biology · 2025Article
- The role of bacterial metabolism in human gut colonization.International microbiology : the official journal of the Spanish Society for Microbiology · 2025Review
- Metabolic modeling of host-microbe interactions.Computational and structural biotechnology journal · 2025Review
- In silico metabolic modelling links microbiome-derived metabolites to risk factors of Alzheimer's disease.Gut microbes reports · 2025Article
67 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The human gut microbiota consists of ten times more microorganisms than there are cells in our body, processes otherwise indigestible nutrients, and produces important energy precursors, essential amino acids, and vitamins. In this study, we assembled and validated a genome-scale metabolic reconstruction of Bacteroides thetaiotaomicron (iAH991), a prominent representative of the human gut microbiota, consisting of 1488 reactions, 1152 metabolites, and 991 genes. To create a comprehensive metabolic model of host-microbe interactions, we integrated iAH991 with a previously published mouse metabolic reconstruction, which was extended for intestinal transport and absorption reactions. The two metabolic models were linked through a joint compartment, the lumen, allowing metabolite exchange and providing a route for simulating different dietary regimes. The resulting model consists of 7239 reactions, 5164 metabolites, and 2769 genes. We simultaneously modeled growth of mouse and B. thetaiotaomicron on five different diets varying in fat, carbohydrate, and protein content. The integrated model captured mutually beneficial cross-feeding as well as competitive interactions. Furthermore, we identified metabolites that were exchanged between the two organisms, which were compared with published metabolomics data. This analysis resulted for the first time in a comprehensive description of the co-metabolism between a host and its commensal microbe. We also demonstrate in silico that the presence of B. thetaiotaomicron could rescue the growth phenotype of the host with an otherwise lethal enzymopathy and vice versa. This systems approach represents a powerful tool for modeling metabolic interactions between a gut microbe and its host in health and disease.
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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.