ReviewBiochemical Society transactions2018
Review and perspective on mathematical modeling of microbial ecosystems.
Review in Biochemical Society transactions, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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.
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Who cites it
29 citing papers in PubMed.
- Article
- Traditional fermented food microbial ecosystems oriented towards industrial standards: multi-dimensional characterization and artificial regulation.NPJ science of food · 2026Review
- Predictive multispecies constraint-based metabolic modeling: case studies and best practices.Briefings in bioinformatics · 2026Review
- Personalized Constraint-Based Modeling of Microbial Communities from Metagenomic Data.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Identification of dynamic models of microbial communities: A workflow addressing identifiability and modeling pitfalls.PLoS computational biology · 2025Article
- Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.Briefings in bioinformatics · 2025Review
- Deciphering and designing microbial communities by genome-scale metabolic modelling.Computational and structural biotechnology journal · 2024Review
- Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based kMicrobial cell factories · 2024Article
- Population Response of Rhizosphere Microbiota of Garden Pea Genotypes to Inoculation with Arbuscular Mycorrhizal Fungi.International journal of molecular sciences · 2023Article
- Calibrating spatiotemporal models of microbial communities to microscopy data: A review.PLoS computational biology · 2022Review
- Species abundance correlations carry limited information about microbial network interactions.PLoS computational biology · 2022Article
- Complex and unexpected outcomes of antibiotic therapy against a polymicrobial infection.The ISME journal · 2022Article
- Article
- Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals.PLoS computational biology · 2021Article
- Modelling microbial communities: Harnessing consortia for biotechnological applications.Computational and structural biotechnology journal · 2021Review
- Dynamics of microbial competition, commensalism, and cooperation and its implications for coculture and microbiome engineering.Biotechnology and bioengineering · 2021Article
- Metabolic modelling approaches for describing and engineering microbial communities.Computational and structural biotechnology journal · 2021Review
- Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology.Frontiers in microbiology · 2021Article
- From sequence to information.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Review
- Future directions for studying resilience of the oral ecosystem.British dental journal · 2020Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding microbial ecosystems means unlocking the path toward a deeper knowledge of the fundamental mechanisms of life. Engineered microbial communities are also extremely relevant to tackling some of today's grand societal challenges. Advanced meta-omics experimental techniques provide crucial insights into microbial communities, but have been so far mostly used for descriptive, exploratory approaches to answer the initial 'who is there?' QUESTION: An ecosystem is a complex network of dynamic spatio-temporal interactions among organisms as well as between organisms and the environment. Mathematical models with their abstraction capability are essential to capture the underlying phenomena and connect the different scales at which these systems act. Differential equation models and constraint-based stoichiometric models are deterministic approaches that can successfully provide a macroscopic description of the outcome from microscopic behaviors. In this mini-review, we present classical and recent applications of these modeling methods and illustrate the potential of their integration. Indeed, approaches that can capture multiple scales are needed in order to understand emergent patterns in ecosystems and their dynamics regulated by different spatio-temporal phenomena. We finally discuss promising examples of methods proposing the integration of differential equations with constraint-based stoichiometric models and argue that more work is needed in this direction.
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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.