ArticleJournal of cellular physiology2016
Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction.
Article in Journal of cellular physiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed.
- Metabolic Modelling Facilitates the Design of Synthetic Communities by Simplifying Natural Microbial Communities.Environmental microbiology · 2026Article
- Review
- Constraint-Based Metabolic Modeling Approach for Microbial Communities.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Article
- Article
- Coupling flux balance analysis with reactive transport modeling through machine learning for rapid and stable simulation of microbial metabolic switching.Scientific reports · 2025Article
- Engineering natural microbiomes toward enhanced bioremediation by microbiome modeling.Nature communications · 2024Article
- Comparative analysis of metabolic models of microbial communities reconstructed from automated tools and consensus approaches.NPJ systems biology and applications · 2024Article
- Article
- Top-down and bottom-up microbiome engineering approaches to enable biomanufacturing from waste biomass.Journal of industrial microbiology & biotechnology · 2024Review
- Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing.Microbial biotechnology · 2024Review
- Plant Growth-Promoting Bacteria of Soil: Designing of Consortia Beneficial for Crop Production.Microorganisms · 2023Review
- Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges.FEMS microbiology ecology · 2023Review
- Analysis of Endophytic Bacterial Communities and Investigation of Core Taxa in Apple Trees.The plant pathology journal · 2023Article
- Cyanobacteria as cell factories for the photosynthetic production of sucrose.Frontiers in microbiology · 2023Review
- Interaction Networks Are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes.mSystems · 2022Article
- Article
- Exploring the roles of microbes in facilitating plant adaptation to climate change.The Biochemical journal · 2022Article
- Application of the Metabolic Modeling Pipeline in KBase to Categorize Reactions, Predict Essential Genes, and Predict Pathways in an Isolate Genome.Methods in molecular biology (Clifton, N.J.) · 2022Article
- A gap-filling algorithm for prediction of metabolic interactions in microbial communities.PLoS computational biology · 2021Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metabolic network modeling of microbial communities provides an in-depth understanding of community-wide metabolic and regulatory processes. Compared to single organism analyses, community metabolic network modeling is more complex because it needs to account for interspecies interactions. To date, most approaches focus on reconstruction of high-quality individual networks so that, when combined, they can predict community behaviors as a result of interspecies interactions. However, this conventional method becomes ineffective for communities whose members are not well characterized and cannot be experimentally interrogated in isolation. Here, we tested a new approach that uses community-level data as a critical input for the network reconstruction process. This method focuses on directly predicting interspecies metabolic interactions in a community, when axenic information is insufficient. We validated our method through the case study of a bacterial photoautotroph-heterotroph consortium that was used to provide data needed for a community-level metabolic network reconstruction. Resulting simulations provided experimentally validated predictions of how a photoautotrophic cyanobacterium supports the growth of an obligate heterotrophic species by providing organic carbon and nitrogen sources. J. Cell. Physiol. 231: 2339-2345, 2016. © 2016 Wiley Periodicals, Inc.
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