ReviewMicrobiome2017
More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes.
Review in Microbiome, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 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
30 citing papers in PubMed.
- Precision nutrition through diet-gut microbiome interactions: Emerging insights driven by artificial intelligence, microbiome health metrics, and mechanistic modeling.Gut microbes reports · 2026Review
- Credible inferences in microbiome research: ensuring rigour, reproducibility and relevance in the era of AI.Nature reviews. Gastroenterology & hepatology · 2025Review
- Understanding disease-associated metabolic changes in human colonic epithelial cells using the iColonEpithelium metabolic reconstruction.PLoS computational biology · 2025Article
- Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition.mSystems · 2024Article
- Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine.Nature biotechnology · 2023Article
- Cancer's second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution.BioEssays : news and reviews in molecular, cellular and developmental biology · 2022Review
- Butyrate Production Pathway Abundances Are Similar in Human and Nonhuman Primate Gut Microbiomes.Molecular biology and evolution · 2022Article
- NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome.Frontiers in bioinformatics · 2022Article
- Metaproteomics reveals insights into microbial structure, interactions, and dynamic regulation in defined communities as they respond to environmental disturbance.BMC microbiology · 2021Article
- An extended reconstruction of human gut microbiota metabolism of dietary compounds.Nature communications · 2021Article
- Development of a Genome-Scale Metabolic Model and Phenome Analysis of the ProbioticInternational journal of molecular sciences · 2021Article
- Advances in flux balance analysis by integrating machine learning and mechanism-based models.Computational and structural biotechnology journal · 2021Review
- A Hybrid Flux Balance Analysis and Machine Learning Pipeline Elucidates Metabolic Adaptation in Cyanobacteria.iScience · 2020Article
- True and Illusory Benefits of Modeling: Comment on "Genome-Scale Metabolic Network Reconstruction and In Silico Analysis of Hexanoic Acid ProducingMicroorganisms · 2020Article
- Evaluation of existing guidelines for their adequacy for the microbial characterisation and environmental risk assessment of microorganisms obtained through synthetic biology.EFSA journal. European Food Safety Authority · 2020Article
- Clustering analysis of tumor metabolic networks.BMC bioinformatics · 2020Article
- Challenges and emerging systems biology approaches to discover how the human gut microbiome impact host physiology.Biophysical reviews · 2020Review
- Computational Modeling of the Human Microbiome.Microorganisms · 2020Review
- From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes.Computational and structural biotechnology journal · 2020Review
- The Use of Defined Microbial Communities To Model Host-Microbe Interactions in the Human Gut.Microbiology and molecular biology reviews : MMBR · 2019Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
The human gut is colonized with a myriad of microbes, with substantial interpersonal variation. This complex ecosystem is an integral part of the gastrointestinal tract and plays a major role in the maintenance of homeostasis. Its dysfunction has been correlated to a wide array of diseases, but the understanding of causal mechanisms is hampered by the limited amount of cultured microbes, poor understanding of phenotypes, and the limited knowledge about interspecies interactions. Genome-scale metabolic models (GEMs) have been used in many different fields, ranging from metabolic engineering to the prediction of interspecies interactions. We provide showcase examples for the application of GEMs for gut microbes and focus on (i) the prediction of minimal, synthetic, or defined media; (ii) the prediction of possible functions and phenotypes; and (iii) the prediction of interspecies interactions. All three applications are key in understanding the role of individual species in the gut ecosystem as well as the role of the microbiota as a whole. Using GEMs in the described fashions has led to designs of minimal growth media, an increased understanding of microbial phenotypes and their influence on the host immune system, and dietary interventions to improve human health. Ultimately, an increased understanding of the gut ecosystem will enable targeted interventions in gut microbial composition to restore homeostasis and appropriate host-microbe crosstalk.
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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.