GutLogo: Agent-based modeling framework to investigate spatial and temporal dynamics in the gut microbiome

Authored by Charlie Lin, Joshua Culver, Bronson Weston, Evan Underhill, Jonathan Gorky, Prasad Dhurjati

Date Published: 2018

DOI: 10.1371/journal.pone.0207072

Sponsors: No sponsors listed

Platforms: NetLogo

Model Documentation: Other Narrative

Model Code URLs: https://github.com/GutLogo/GutLogo

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.

Tags

environment health Strains Bifidobacteria Oligosaccharides Clostridium-difficile Bacterial-growth Autism Bacteroides