ArticlemSystems2021
Enhancing Microbiome Research through Genome-Scale Metabolic Modeling.
Article in mSystems, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
28 citing papers in PubMed.
- Metabolic Engineering for Gibberellic Acid Production inMolecules (Basel, Switzerland) · 2026Review
- Genome-Scale Metabolic Models Guided Improvement of Fermented Milk Quality and Flavor byFoods (Basel, Switzerland) · 2026Article
- Dynamical Systems-Constrained Metabolic Modeling Enables Forecasting of Host-Microbiome Dynamics.bioRxiv : the preprint server for biology · 2026Article
- Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.NPJ biofilms and microbiomes · 2026Review
- Substrate utilization and cross-feeding synergistically determine microbiome resistance to pathogen invasion.Nature ecology & evolution · 2026Article
- Computational and multi-omics systems biology for precision microbiome therapeutics.Frontiers in microbiomes · 2026Review
- Research Progress on the Adaptation Law and Core Mechanism of Animal Models for Exercise Intervention in Inflammatory Bowel Disease: A Systematic Review.Clinical and experimental gastroenterology · 2026Review
- Metagenomics-Toolkit: the flexible and efficient cloud-based metagenomics workflow featuring machine learning-enabled resource allocation.NAR genomics and bioinformatics · 2025Article
- Article
- The role of bacterial metabolism in human gut colonization.International microbiology : the official journal of the Spanish Society for Microbiology · 2025Review
- Soil biodiversity and function under global change.PLoS biology · 2025Review
- Modeling bacterial interactions uncovers the importance of outliers in the coastal lignin-degrading consortium.Nature communications · 2025Article
- PredCMB: predicting changes in microbial metabolites based on the gene-metabolite network analysis of shotgun metagenome data.Bioinformatics (Oxford, England) · 2024Article
- EnzChemRED, a rich enzyme chemistry relation extraction dataset.Scientific data · 2024Article
- Improving the odds: Artificial intelligence and the great plate count anomaly.Microbial biotechnology · 2024Article
- Engineering Gut Symbionts: A Way to Promote Bee Growth?Insects · 2024Review
- Flux sampling in genome-scale metabolic modeling of microbial communities.BMC bioinformatics · 2024Article
- Evaluating E. coli genome-scale metabolic model accuracy with high-throughput mutant fitness data.Molecular systems biology · 2023Article
- Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations.Briefings in bioinformatics · 2023Review
- Recent advances in data- and knowledge-driven approaches to explore primary microbial metabolism.Current opinion in chemical biology · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
Construction and analysis of genome-scale metabolic models (GEMs) is a well-established systems biology approach that can be used to predict metabolic and growth phenotypes. The ability of GEMs to produce mechanistic insight into microbial ecological processes makes them appealing tools that can open a range of exciting opportunities in microbiome research. Here, we briefly outline these opportunities, present current rate-limiting challenges for the trustworthy application of GEMs to microbiome research, and suggest approaches for moving the field forward.
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What OpenQuestion holds
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.