ArticleNPJ systems biology and applications2021
Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis.
Article in NPJ systems biology and applications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 papers.
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Who cites it
53 citing papers in PubMed, 92 citations in OpenAlex.
- Personalized whole-body modeling links gut microbiota to metabolic perturbations in Alzheimer's disease.Gut microbes · 2026Article
- Microbiota-Associated Amino Acid Metabolites in Inflammatory Bowel Disease: Emerging Key Players in the Host-Microbe Interface.Microorganisms · 2026Review
- Integrating host-microbiome multi-omics with machine learning: methods, benchmarks, and translational applications.Science China. Life sciences · 2026Review
- Research advances in the identification of gut keystone bacteria and formulation of suitable dietary intervention strategies for restoring gut homeostasis.NPJ biofilms and microbiomes · 2026Review
- Gut Microbiota in Irritable Bowel Syndrome and Inflammatory Bowel Disease: Differences in Pathophysiology, Biomarkers, and Treatment Implications.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Article
- Personalized Constraint-Based Modeling of Microbial Communities from Metagenomic Data.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Article
- Integrating gut microbiota and metabolomics in pediatric inflammatory bowel disease: insights into pathogenesis and potential role of precision medicine.European journal of medical research · 2025Review
- Genome-scale metabolic modelling of human gut microbes to inform rational community design.Gut microbes · 2025Article
- Metabolic modeling links gut microbiota to metabolic markers of Parkinson's disease.Gut microbes · 2025Article
- Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation.Microbiome · 2025Article
- Systems biology and microbiome innovations for personalized diabetic retinopathy management.NPJ systems biology and applications · 2025Review
- Severity of atopic dermatitis is associated with gut-derived metabolites and leaky gut-related biomarkers.Scientific reports · 2025Article
- Genome-scale metabolic model-guided systematic framework for designing customized live biotherapeutic products.NPJ systems biology and applications · 2025Review
- Metabolic modeling reveals a multi-level deregulation of host-microbiome metabolic networks in IBD.Nature communications · 2025Article
- Microbes with higher metabolic independence are enriched in human gut microbiomes under stress.eLife · 2025Article
- Review
- In silico metabolic modelling links microbiome-derived metabolites to risk factors of Alzheimer's disease.Gut microbes reports · 2025Article
- Balancing Oxidative Stress: How the Gut Microbiome Supports Redox Homeostasis and Mitochondrial Health.Journal of restorative medicine · 2025Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Inflammatory bowel diseases, such as Crohn's Disease, are characterised by an altered blood and faecal metabolome, and changes in gut microbiome composition. Here, we present an efficient, scalable, tractable systems biology framework to mechanistically link microbial strains and faecal metabolites. We retrieve strain-level relative abundances from metagenomics data from a cohort of paediatric Crohn's Disease patients with and without dysbiosis and healthy control children and construct and interrogate a personalised microbiome model for each sample. Predicted faecal secretion profiles and strain-level contributions to each metabolite vary broadly between healthy, dysbiotic, and non-dysbiotic microbiomes. The reduced microbial diversity in IBD results in reduced numbers of secreted metabolites, especially in sulfur metabolism. We demonstrate that increased potential to synthesise amino acids is linked to Proteobacteria contributions, in agreement with experimental observations. The established modelling framework yields testable hypotheses that may result in novel therapeutic and dietary interventions targeting the host-gut microbiome-diet axis.
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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.