Related Experiment Video
Updated: Feb 2, 2026
09:18
A Gut-on-a-Chip Model to Study the Gut Microbiome-Nervous System Axis
Published on: July 28, 2023
3.5K
GutLogo: Agent-based modeling framework to investigate spatial and temporal dynamics in the gut microbiome.
Charlie Lin1, Joshua Culver1, Bronson Weston1
1Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, United States of America.
Plos One
|November 10, 2018
Summary
Understanding gut microbiome dynamics is key to human health. A new agent-based model, GutLogo, simulates bacterial populations in the ileum, aiding in studying health and disease.
Area of Science:
- Microbiology
- Computational Biology
- Systems Biology
Background:
- The gut microbiome's spatial and temporal dynamics are crucial for human health, with alterations linked to numerous diseases.
- Studying these dynamics in vivo or in vitro is challenging due to microbiome complexity.
- In silico experiments offer a viable alternative for investigating gut microbial systems.
Purpose of the Study:
- To develop a user-friendly agent-based model, GutLogo, for simulating the spatial and temporal dynamics of key bacterial genera in the ileum.
- To assess the model's utility by simulating responses to various physiological perturbations.
Main Methods:
- Development of GutLogo, an agent-based model.
- Simulation of four representative bacterial genera populations in the ileum.
- Perturbation analysis including changes in flow rate, nutrition, and probiotic introduction.
Main Results:
- The GutLogo model successfully captured spatial and temporal bacterial population dynamics.
- Simulations showed distinct population level changes in response to flow rate, nutrition, and probiotic perturbations.
- Most simulated gut populations demonstrated resilience, returning to steady states after disturbances ceased.
Conclusions:
- GutLogo provides a valuable framework for in silico investigation of gut microbiome dynamics.
- The model can be extended to simulate diverse physiological scenarios and incorporate additional complexities.
- This computational approach aids in understanding gut health and disease-related microbial shifts.
Related Concept Videos
02:20Dynamic Equilibrium
62.7K
A reversible chemical reaction represents a chemical process that proceeds in both forward (left to right) and reverse (right to left) directions. When the rates of the forward and reverse reactions are equal, the concentrations of the reactant and product species remain constant over time and the system is at equilibrium. A special double arrow is used to emphasize the reversible nature of the reaction. The relative concentrations of reactants and products in equilibrium systems vary greatly;...
62.7K
01:29Subviral Agents
565
Subviral agents are infectious entities that resemble viruses but lack one or more viral components, such as a capsid or essential replication machinery. These agents include viroids, prions, and satellites, each possessing distinct structural and functional characteristics that influence their mode of infection and replication.Viroids are the simplest subviral agents, consisting of circular, single-stranded RNA molecules without a protein coat. They exclusively infect plants, relying entirely...
565
01:10¹H NMR of Labile Protons: Temporal Resolution
1.7K
Protons bonded to heteroatoms such as nitrogen and oxygen exhibit a range of chemical shift values. This is due to the varying degree of hydrogen bonding between the proton and the heteroatom in other molecules. The extent of hydrogen bonding affects the electron density around the proton, thereby giving different chemical shift values for the protons in the proton NMR spectrum.
The –OH proton in alcohols typically appears in the range of δ 2 to 5 ppm but can vary depending on the specific...
The –OH proton in alcohols typically appears in the range of δ 2 to 5 ppm but can vary depending on the specific...
1.7K
01:27Air-entraining Agents
272
Air-entraining agents improve the durability and workability of concrete in climates with frequent freezing and thawing. These agents prevent cracks by introducing small air bubbles into the mix, creating spaces accommodating water expansion when temperatures drop. The air-entraining agents lower the surface tension of water, forming stable, small air bubbles. This method is more effective than having accidental large voids, as the intentional, smaller, and evenly distributed air voids improve...
272
01:15Depth Perception and Spatial Vision
2.0K
Depth perception is the ability to perceive objects three-dimensionally. It relies on two types of cues: binocular and monocular. Binocular cues depend on the combination of images from both eyes and how the eyes work together. Since the eyes are in slightly different positions, each eye captures a slightly different image. This disparity between images, known as binocular disparity, helps the brain interpret depth. When the brain compares these images, it determines the distance to an object.
2.0K
01:19Assessing Body Temperature - Temporal Artery
1.2K
Here is a stepwise guide to assessing the body temperature at the temporal artery using a temporal artery thermometer
Step 1: Perform hand hygiene and don a fresh pair of gloves to prevent cross-infection and ensure patient safety.
Step 2: Explain the procedure to the patient to establish trust. Clear communication establishes trust with the patient, ensures they understand what to expect, promotes cooperation, and enhances comfort during the procedure.
Step 3: Assess the patient's...
Step 1: Perform hand hygiene and don a fresh pair of gloves to prevent cross-infection and ensure patient safety.
Step 2: Explain the procedure to the patient to establish trust. Clear communication establishes trust with the patient, ensures they understand what to expect, promotes cooperation, and enhances comfort during the procedure.
Step 3: Assess the patient's...
1.2K