ArticleGut microbes
Integration of constraint-based modeling with fecal metabolomics reveals large deleterious effects of
Article in Gut microbes. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 35 citations in OpenAlex.
- Article
- Modeling diet-gut microbiome interactions and prebiotic responses in Thai adults.NPJ biofilms and microbiomes · 2026Article
- Interkingdom microbiome physiology in colorectal cancer: barrier dysfunction, immune-metabolic signaling, and therapeutic resistance.Frontiers in physiology · 2026Review
- Toward the Next Generation of In Silico Modeling of Dynamic Host-Microbiota Interactions in the Skin.JID innovations : skin science from molecules to population health · 2025Review
- Alterations in the Gut Microbiota and Metabolite Profiles of Lung Cancer Patients.Current microbiology · 2025Article
- Characterising functional redundancy in microbiome communities via relative entropy.Computational and structural biotechnology journal · 2025Article
- Personalized modeling of gut microbiome metabolism throughout the first year of life.Communications medicine · 2024Article
- Genome-scale community modelling elucidates the metabolic interaction in Indian type-2 diabetic gut microbiota.Scientific reports · 2024Article
- Genome-resolved metagenomics: a game changer for microbiome medicine.Experimental & molecular medicine · 2024Review
- The multispecies microbial cluster of Fusobacterium, Parvimonas, Bacteroides and Faecalibacterium as a precision biomarker for colorectal cancer diagnosis.Molecular oncology · 2024Article
- Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer's disease.Scientific reports · 2024Article
- Causal inference on microbiome-metabolome relations in observational host-microbiome data via in silico in vivo association pattern analyses.Cell reports methods · 2023Article
- Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine.Nature biotechnology · 2023Article
- Recent advances in data- and knowledge-driven approaches to explore primary microbial metabolism.Current opinion in chemical biology · 2023Review
- pymgpipe: microbiome metabolic modeling in Python.Journal of open source software · 2023Article
- Taxonomic and functional profiling of fecal metagenomes for the early detection of colorectal cancer.Frontiers in oncology · 2023Article
- Enteric nervous system damage caused by abnormal intestinal butyrate metabolism may lead to functional constipation.Frontiers in microbiology · 2023Article
- Review
- The gut microbial metabolite formate exacerbates colorectal cancer progression.Nature metabolism · 2022Article
- Article
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
Characterizing the metabolic functions of the gut microbiome in health and disease is pivotal for translating alterations in microbial composition into clinical insights. Two major analysis paradigms have been used to explore the metabolic functions of the microbiome but not systematically integrated with each other: statistical screening approaches, such as metabolome-microbiome association studies, and computational approaches, such as constraint-based metabolic modeling. To combine the strengths of the two analysis paradigms, we herein introduce a set of theoretical concepts allowing for the population statistical treatment of constraint-based microbial community models. To demonstrate the utility of the theoretical framework, we applied it to a public metagenomic dataset consisting of 365 colorectal cancer (CRC) cases and 251 healthy controls, shining a light on the metabolic role of
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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.