ArticlePloS one2018
GutLogo: Agent-based modeling framework to investigate spatial and temporal dynamics in the gut microbiome.
Article in PloS one, 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.
- Systems engineering of engineered live biotherapeutics: A discovery-to-translation framework for streamlining microbiome therapeutic development.Journal of controlled release : official journal of the Controlled Release Society · 2026Review
- Virtual Colon: spatiotemporal modeling of metabolic interactions in a computational colonic environment.mSystems · 2026Article
- Computational and multi-omics systems biology for precision microbiome therapeutics.Frontiers in microbiomes · 2026Review
- Agent-based model of the human colon to investigate mechanisms of pathogen colonization resistance.Biophysical journal · 2025Article
- Control of medical digital twins with artificial neural networks.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2025Article
- Colon or semicolon: gut sampling microdevices for omics insights.NPJ biofilms and microbiomes · 2024Review
- Metabolic interactions shape emergent biofilm structures in a conceptual model of gut mucosal bacterial communities.NPJ biofilms and microbiomes · 2024Article
- Feasibility of engineeredBioengineering & translational medicine · 2024Article
- Article
- NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome.Frontiers in bioinformatics · 2022Article
- Emerging computational paradigms to address the complex role of gut microbial metabolism in cardiovascular diseases.Frontiers in cardiovascular medicine · 2022Review
- Modeling approaches for probing cross-feeding interactions in the human gut microbiome.Computational and structural biotechnology journal · 2022Review
- Agent Based Models of Polymicrobial Biofilms and the Microbiome-A Review.Microorganisms · 2021Review
- Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions.Frontiers in microbiology · 2021Article
- Computational Modeling of the Human Microbiome.Microorganisms · 2020Review
- Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling tools.Computational and structural biotechnology journal · 2020Review
- Agent-based models of inflammation in translational systems biology: A decade later.Wiley interdisciplinary reviews. Systems biology and medicine · 2019Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Knowledge of the spatial and temporal dynamics of the gut microbiome is essential to understanding the state of human health, as over a hundred diseases have been correlated with changes in microbial populations. Unfortunately, due to the complexity of the microbiome and the limitations of in vivo and in vitro experiments, studying spatial and temporal dynamics of gut bacteria in a biological setting is extremely challenging. Thus, in silico experiments present an excellent alternative for studying such systems. In consideration of these issues, we have developed a user-friendly agent-based model, GutLogo, that captures the spatial and temporal development of four representative bacterial genera populations in the ileum. We demonstrate the utility of this model by simulating population responses to perturbations in flow rate, nutrition, and probiotics. While our model predicts distinct changes in population levels due to these perturbations, most of the simulations suggest that the gut populations will return to their original steady states once the disturbance is removed. We hope that, in the future, the GutLogo model is utilized and customized by interested parties, as GutLogo can serve as a basic modeling framework for simulating a variety of physiological scenarios and can be extended to capture additional complexities of interest.
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Registered trials
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