ArticleBMC systems biology2018
Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss.
Article in BMC systems biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Metabolic Modeling ofMetabolites · 2023Article
- Prevalent emergence of reciprocity among cross-feeding bacteria.ISME communications · 2022Article
- Integrative Gene Expression and Metabolic Analysis ToolBiomolecules · 2022Article
- Review
- Modeling approaches for probing cross-feeding interactions in the human gut microbiome.Computational and structural biotechnology journal · 2022Review
- Diversity begets diversity during community assembly until ecological limits impose a diversity ceiling.Molecular ecology · 2021Article
- Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the genusMicrobial genomics · 2020Article
- The microbial exometabolome: ecological resource and architect of microbial communities.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Review
- Multi-faceted approaches to discovering and predicting microbial nutritional interactions.Current opinion in biotechnology · 2020Review
- From Microbial Communities to Distributed Computing Systems.Frontiers in bioengineering and biotechnology · 2020Review
- Ignoring social distancing: advances in understanding multi-species bacterial interactions.Faculty reviews · 2020Review
- Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies.mSystems · 2019Article
- Syntrophy emerges spontaneously in complex metabolic systems.PLoS computational biology · 2019Article
- Current status and applications of genome-scale metabolic models.Genome biology · 2019Review
- Bottom-Up Approaches to Synthetic Cooperation in Microbial Communities.Life (Basel, Switzerland) · 2019Review
- An enormous potential for niche construction through bacterial cross-feeding in a homogeneous environment.PLoS computational biology · 2018Article
- Article
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2 authors.
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Abstract
backgroundMetabolic dependencies between microbial species have a significant impact on the assembly and activity of microbial communities. However, the evolutionary origins of such dependencies and the impact of metabolic and genomic architecture on their emergence are not clear.
resultsTo address these questions, we developed a novel framework, coupling a reductive evolution model with a multi-species genome-scale metabolic model to simulate the evolution of two-species microbial communities. Simulating thousands of independent evolutionary trajectories, we surprisingly found that under certain environmental and evolutionary settings metabolic dependencies emerged frequently even though our model does not include explicit selection for cooperation. Evolved dependencies involved cross-feeding of a diverse set of metabolites, reflecting constraints imposed by metabolic network architecture. We additionally found metabolic 'missed opportunities', wherein species failed to capitalize on metabolites made available by their partners. Examining the genes deleted in each evolutionary trajectory and the deletion timing further revealed both genome-wide properties and specific metabolic mechanisms associated with species interaction.
conclusionOur findings provide insight into the evolution of cooperative interaction among microbial species and a unique view into the way such relationships emerge.
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