ArticleNature communications2025
Metabolic modeling reveals a multi-level deregulation of host-microbiome metabolic networks in IBD.
Article in Nature communications, 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 42 papers.
What it found
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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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
42 citing papers in PubMed.
- Genome-scale metabolic models predict diet- and lifestyle-driven shifts of ecological interactions in the gut microbiome.Gut microbes · 2026Article
- Microbiome-based therapeutics forGut microbes · 2026Review
- The gut microbiota-tryptophan metabolism-immune axis in inflammatory bowel disease: Mechanisms and therapeutic prospects.Human vaccines & immunotherapeutics · 2026Review
- Microbiota-Associated Amino Acid Metabolites in Inflammatory Bowel Disease: Emerging Key Players in the Host-Microbe Interface.Microorganisms · 2026Review
- Multi-Compartment Metabolic Remodeling in DRA-Deficient Mice Overlaps with Ulcerative Colitis Metabolic Signatures.Metabolites · 2026Article
- Antisense transcription reveals disease-associated adaptations in the human gut microbiome.Nature microbiology · 2026Article
- Microbiota-derived 4-HPAA alleviates Crohn's disease by stabilizing SIRT1 and reprogramming macrophage immunometabolism.Apoptosis : an international journal on programmed cell death · 2026Article
- From Multi-Omics to Molecular Causality: A Five-Tier Evidence Framework for the Single-Bacterium-Metabolite Axis in IBD.Microorganisms · 2026Review
- Tracing NADCell reports · 2026Article
- Strain-Specific Effects ofMicroorganisms · 2026Article
- Metabolic Profiling of the Gut-Brain Axis in a Murine Model of Ulcerative Colitis with Raman Spectroscopy.ACS applied materials & interfaces · 2026Article
- Bioinspired microcapsule reactor with engineered probiotics for IBD therapy.Nature communications · 2026Article
- Rewriting Inflammation in IBD: Lipidomics from Pathogenesis to Clinical Application.Microorganisms · 2026Review
- Article
- The Gut-Pancreas Axis in Type 1 Diabetes: Emerging Insights into Microbiota and Immune Interactions.International journal of molecular sciences · 2026Review
- Gut Microbiota in Irritable Bowel Syndrome and Inflammatory Bowel Disease: Differences in Pathophysiology, Biomarkers, and Treatment Implications.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Individual variability shapes ex vivo responses to resistant starch in inflammatory bowel disease derived microbiomes.NPJ biofilms and microbiomes · 2026Article
- A metabolic constraint in de novo NAD+ synthesis drives mucosal inflammation in IBD.Journal of Crohn's & colitis · 2026Article
- Novel Insights Into the Association Between Parkinson's Disease and Constipation: Role of SHMT2 as a Promising Biomarker.CNS neuroscience & therapeutics · 2026Article
- Gut Microbiome in Obesity: A Narrative Review of Mechanisms, Interventions, and Future Directions.Probiotics and antimicrobial proteins · 2026Review
Corrections and comments
- Erratum issued
Authors and funding
9 authors.
Funding
Abstract
Inflammatory bowel diseases (IBDs) are chronic disorders involving dysregulated immune responses. Despite the role of disrupted host-microbial interaction in the pathophysiology of IBD, the underlying metabolic principles are not fully understood. We densely profiled microbiome, transcriptome and metabolome signatures from longitudinal IBD cohorts before and after advanced drug therapy initiation and reconstructed metabolic models of the gut microbiome and the host intestine to study host-microbiome metabolic cross-talk in the context of inflammation. Here, we identified concomitant changes in metabolic activity across data layers involving NAD, amino acid, one-carbon and phospholipid metabolism. In particular on the host level, elevated tryptophan catabolism depleted circulating tryptophan, thereby impairing NAD biosynthesis. Reduced host transamination reactions disrupted nitrogen homeostasis and polyamine/glutathione metabolism. The suppressed one-carbon cycle in patient tissues altered phospholipid profiles due to limited choline availability. Simultaneously, microbiome metabolic shifts in NAD, amino acid and polyamine metabolism exacerbated these host metabolic imbalances. Leveraging host and microbe metabolic models, we predicted dietary interventions remodeling the microbiome to restore metabolic homeostasis, suggesting novel therapeutic strategies for IBD.
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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 Socratic graph.