ArticleNPJ biofilms and microbiomes2024
Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities.
Article in NPJ biofilms and microbiomes, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Microphysiological models of human gastrointestinal diseases.Nature biomedical engineering · 2026Review
- Decreased carbohydrate sources reduce microbial diversity and taxonomic redundancy in the murine gut.Microbiology spectrum · 2026Article
- A multi-strain biofilm consortium enhances gut microbiota resilience and restores post-antibiotic homeostasis.World journal of microbiology & biotechnology · 2026Article
- A composite medium enabling co-culture ofMethodsX · 2026Article
- Adaptation ofmSystems · 2026Article
- Microbial Interactions Shape Spatial Organisation and Transcriptional Responses in a Model Mixed-Species Biofilm.Microbial ecology · 2026Article
- Unique ecology of co-occurring functionally and phylogenetically undescribed species in the infant oral microbiome.PLoS computational biology · 2026Article
- Functional potential of archaeal KEGG enzymes in the Moringa oleifera rhizosphere revealed by metagenomic analysis.BMC genomics · 2026Article
- Metabolic interactions between bacterial co-isolates from catheter-associated urinary tract infections.Scientific reports · 2026Article
- Carbon substrate type shapes spatial self-organization in a multi-species biofilm community.The ISME journal · 2026Article
- Bayesian inference captures metabolite-bacteria interactions in a microbial community.ISME communications · 2026Article
- Mixed-species biofilms in food systems: from community assembly to ecology-informed management.Frontiers in microbiology · 2026Review
- Reduced carbohydrate complexity alters gut microbial structure independent of total carbohydrate intake.bioRxiv : the preprint server for biology · 2025Article
- Gut Dysbiosis Driven byGenes · 2025Review
- 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
- Experimental systems are essential for strengthening ecological modeling of microbiomes beyond observational data.mSystems · 2025Review
- Article
- Insights into the Interaction BetweenJournal of personalized medicine · 2025Review
- Mathematical models of the colonic microbiota: an evaluation of accuracy usingFrontiers in nutrition · 2025Article
- Soil fungal community and co-occurrence network patterns at different successional stages of black locust coppice stands.Frontiers in microbiology · 2025Article
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The gut microbiome plays a major role in human health; however, little is known about the structural arrangement of microbes and factors governing their distribution. In this work, we present an in silico agent-based model (ABM) to conceptually simulate the dynamics of gut mucosal bacterial communities. We explored how various types of metabolic interactions, including competition, neutralism, commensalism, and mutualism, affect community structure, through nutrient consumption and metabolite exchange. Results showed that, across scenarios with different initial species abundances, cross-feeding promotes species coexistence. Morphologically, competition and neutralism resulted in segregation, while mutualism and commensalism fostered high intermixing. In addition, cooperative relations resulted in community properties with little sensitivity to the selective uptake of metabolites produced by the host. Moreover, metabolic interactions strongly influenced colonization success following the invasion of newcomer species. These results provide important insights into the utility of ABM in deciphering complex microbiome patterns.
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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 Socratic graph.