ArticlePLoS computational biology2017
BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities.
Article in PLoS computational biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 152 papers.
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Who cites it
152 citing papers in PubMed, 309 citations in OpenAlex.
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- Metabolic set theory: a generalized model of microbial interactions.NPJ systems biology and applications · 2026Article
- Modelling the role of the microbiome in antimicrobial resistance across scales.Nature microbiology · 2026Review
- MOFA: microbial optimization without forced altruism.BMC bioinformatics · 2026Article
- An ecology-driven microbial consortium enhances plant growth and immunity while sustaining rhizospheric microbial balance.Plant communications · 2026Article
- Predictive multispecies constraint-based metabolic modeling: case studies and best practices.Briefings in bioinformatics · 2026Review
- Dynamic metabolic modelling of ATP allocation during viral infection.Journal of the Royal Society, Interface · 2026Article
- Virtual Colon: spatiotemporal modeling of metabolic interactions in a computational colonic environment.mSystems · 2026Article
- Carbon substrate type shapes spatial self-organization in a multi-species biofilm community.The ISME journal · 2026Article
- Spatial structure: shaping the ecology and evolution of microbial communities.FEMS microbiology reviews · 2026Review
- Precision nutrition through diet-gut microbiome interactions: Emerging insights driven by artificial intelligence, microbiome health metrics, and mechanistic modeling.Gut microbes reports · 2026Review
- From Single Organisms to Communities: Modeling Methanotrophs and Their Satellites.Microorganisms · 2025Review
- Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation.Microbiome · 2025Article
- Article
- Metatranscriptomics-based metabolic modeling of patient-specific urinary microbiome during infection.NPJ biofilms and microbiomes · 2025Article
- Toward the Next Generation of In Silico Modeling of Dynamic Host-Microbiota Interactions in the Skin.JID innovations : skin science from molecules to population health · 2025Review
- Biophysical metabolic modeling of complex bacterial colony morphology.Cell systems · 2025Article
- Experimental systems are essential for strengthening ecological modeling of microbiomes beyond observational data.mSystems · 2025Review
92 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances focusing on the metabolic interactions within and between cellular populations have emphasized the importance of microbial communities for human health. Constraint-based modeling, with flux balance analysis in particular, has been established as a key approach for studying microbial metabolism, whereas individual-based modeling has been commonly used to study complex dynamics between interacting organisms. In this study, we combine both techniques into the R package BacArena (https://cran.r-project.org/package=BacArena) to generate novel biological insights into Pseudomonas aeruginosa biofilm formation as well as a seven species model community of the human gut. For our P. aeruginosa model, we found that cross-feeding of fermentation products cause a spatial differentiation of emerging metabolic phenotypes in the biofilm over time. In the human gut model community, we found that spatial gradients of mucus glycans are important for niche formations which shape the overall community structure. Additionally, we could provide novel hypothesis concerning the metabolic interactions between the microbes. These results demonstrate the importance of spatial and temporal multi-scale modeling approaches such as BacArena.
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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.