ReviewJournal of the Royal Society, Interface2016
Constraint-based stoichiometric modelling from single organisms to microbial communities.
Review in Journal of the Royal Society, Interface, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 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.
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Who cites it
60 citing papers in PubMed.
- MOFA: microbial optimization without forced altruism.BMC bioinformatics · 2026Article
- Computational and multi-omics systems biology for precision microbiome therapeutics.Frontiers in microbiomes · 2026Review
- Personalized Constraint-Based Modeling of Microbial Communities from Metagenomic Data.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Reducing redundancy and enhancing accuracy through a phylogenetically-informed microbial community metabolic modeling approach.Bioinformatics (Oxford, England) · 2025Article
- MACAW: a method for semi-automatic detection of errors in genome-scale metabolic models.Genome biology · 2025Article
- The proteome is a terminal electron acceptor.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Biotechnology systems engineering: preparing the next generation of bioengineers.Frontiers in systems biology · 2025Article
- Deciphering and designing microbial communities by genome-scale metabolic modelling.Computational and structural biotechnology journal · 2024Review
- Genome-scale model ofMicrobiology spectrum · 2024Article
- Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition.mSystems · 2024Article
- Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics.Microbiology spectrum · 2024Article
- Probing interspecies metabolic interactions within a synthetic binary microbiome using genome-scale modeling.Microbiome research reports · 2024Article
- Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing.Microbial biotechnology · 2024Review
- Microbiome modeling: a beginner's guide.Frontiers in microbiology · 2024Review
- Searching for Principles of Microbial Ecology Across Levels of Biological Organization.Integrative and comparative biology · 2023Article
- Inferring microbial interactions with their environment from genomic and metagenomic data.PLoS computational biology · 2023Article
- A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia.PLoS computational biology · 2023Article
- Unlocking the magic in mycelium: Using synthetic biology to optimize filamentous fungi for biomanufacturing and sustainability.Materials today. Bio · 2023Article
- Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics.bioRxiv : the preprint server for biology · 2023Article
- A Two-Compartment Fermentation System to Quantify Strain-Specific Interactions in Microbial Co-Cultures.Bioengineering (Basel, Switzerland) · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbial communities are ubiquitously found in Nature and have direct implications for the environment, human health and biotechnology. The species composition and overall function of microbial communities are largely shaped by metabolic interactions such as competition for resources and cross-feeding. Although considerable scientific progress has been made towards mapping and modelling species-level metabolism, elucidating the metabolic exchanges between microorganisms and steering the community dynamics remain an enormous scientific challenge. In view of the complexity, computational models of microbial communities are essential to obtain systems-level understanding of ecosystem functioning. This review discusses the applications and limitations of constraint-based stoichiometric modelling tools, and in particular flux balance analysis (FBA). We explain this approach from first principles and identify the challenges one faces when extending it to communities, and discuss the approaches used in the field in view of these challenges. We distinguish between steady-state and dynamic FBA approaches extended to communities. We conclude that much progress has been made, but many of the challenges are still open.
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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.