ArticlePloS one2017
A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Personalized Constraint-Based Modeling of Microbial Communities from Metagenomic Data.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes.Environmental microbiome · 2025Article
- Article
- Community metabolic modeling of host-microbiota interactions through multi-objective optimization.iScience · 2024Article
- Predicting microbial interactions with approaches based on flux balance analysis: an evaluation.BMC bioinformatics · 2024Article
- Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing.Microbial biotechnology · 2024Review
- Assumptions on decision making and environment can yield multiple steady states in microbial community models.BMC bioinformatics · 2023Article
- scFASTCORMICS: A Contextualization Algorithm to Reconstruct Metabolic Multi-Cell Population Models from Single-Cell RNAseq Data.Metabolites · 2022Article
- Metabolic modeling-based drug repurposing in Glioblastoma.Scientific reports · 2022Article
- Multi-Objective Optimization of Microalgae Metabolism: An Evolutive Algorithm Based on FBA.Metabolites · 2022Article
- Contribution of genome-scale metabolic modelling to niche theory.Ecology letters · 2022Article
- Guided extraction of genome-scale metabolic models for the integration and analysis of omics data.Computational and structural biotechnology journal · 2021Article
- Metabolic modelling approaches for describing and engineering microbial communities.Computational and structural biotechnology journal · 2021Review
- Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the genusMicrobial genomics · 2020Article
- Article
- 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
- Multi-objective Parameter Auto-tuning for Tissue Image Segmentation Workflows.Journal of digital imaging · 2019Article
- Flux sampling is a powerful tool to study metabolism under changing environmental conditions.NPJ systems biology and applications · 2019Article
- Metabolic Modeling of Microbial Community Interactions for Health, Environmental and Biotechnological Applications.Current genomics · 2018Review
- Suboptimal community growth mediated through metabolite crossfeeding promotes species diversity in the gut microbiota.PLoS computational biology · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Interplay within microbial communities impacts ecosystems on several scales, and elucidation of the consequent effects is a difficult task in ecology. In particular, the integration of genome-scale data within quantitative models of microbial ecosystems remains elusive. This study advocates the use of constraint-based modeling to build predictive models from recent high-resolution -omics datasets. Following recent studies that have demonstrated the accuracy of constraint-based models (CBMs) for simulating single-strain metabolic networks, we sought to study microbial ecosystems as a combination of single-strain metabolic networks that exchange nutrients. This study presents two multi-objective extensions of CBMs for modeling communities: multi-objective flux balance analysis (MO-FBA) and multi-objective flux variability analysis (MO-FVA). Both methods were applied to a hot spring mat model ecosystem. As a result, multiple trade-offs between nutrients and growth rates, as well as thermodynamically favorable relative abundances at community level, were emphasized. We expect this approach to be used for integrating genomic information in microbial ecosystems. Following models will provide insights about behaviors (including diversity) that take place at the ecosystem scale.
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Registered trials
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