Computer simulations of the physical properties of the human gut to predict their influence on the microbiome

April 26th, 2023

Using 3-D simulations of the physical and biomechanical properties of the human gut to improve microbiome predictive modelling framework resulting in targeted interventions and better patient outcomes.

The challenge

This clip shows the peristaltic movement of the gut walls of the intestine. This wave-like action is used to squeeze food along the digestive track.

Key to understanding healthy function of the gut is the knowledge of how ingested food materials progressively break down mechanically, chemically, and microbiologically to provide nutrient bioavailability for the body’s needs. The gut microbiome is an important part of this, playing many vital health roles: metabolising indigestible carbohydrates for additional energy recovery; short-chain fatty acid production that aids immune system regulation and provides many additional health benefits; and resistance to pathogen invasion. Understanding how diet and gastrointestinal physiology and behaviour impacts a given person’s microbiome will inform targeted interventions or therapies in the future.

The human gut is difficult to characterise experimentally except where highly invasive methods are used. Bench-top experiments are often used to study digestion of food structures and metabolite production for a sampled microbiome, but are heavily idealised and poorly represent the real mechanical environment of the human gut.

Our response

Video of a 3-D model of the mouth chewing

CSIRO researchers are developing dynamic, physics-based, 3D simulations that can provide insights into factors impacting the gut microbiome in scenarios where experimentation is not practical. Further, by incorporating the physical and biomechanical properties of the human gut into predictive model frameworks, the influence of these on the microbiome can be taken into account. Gut simulations will use a combination of particle-based models of fluids, solids and particulates with biophysical models of gastrointestinal physiology to represent the real in-body environment. These models will progressively incorporate models of microbiome communities and their metabolic activity. Once developed, these models can be used to investigate, for example:

  • The effect of food breakdown, transport and mixing on microbial community structure and metabolic function along the gastrointestinal tract.
  • How dynamics of colon physiology (haustral geometry, wall movements, mucus secretion/thickness) influence digesta flow and biofilm formation/dispersal.
  • Interactions between microbial species that influence community structure.

By using computer simulations to develop novel insights into which physical mechanisms influence or modify microbial communities, this knowledge may potentially inform new targeted interventions for greater microbiome control and enhanced health outcomes.

By David Spadaro


Flow processes occurring within the body but still external to the body’s epithelial layer (gastrointestinal and respiratory tracts)

Peristaltic transport of a particulate suspension in the small intestine

Investigating the relationships between peristaltic contraction and fluid transport in the human colon using Smoothed Particle Hydrodynamics

Modelling food digestion

Investigating mixing and emptying for aqueous liquid content from the stomach using a coupled biomechanical-SPH model

A particle-based modelling approach to food processing operations – ScienceDirect

The team

Dr Shaktivesh Shaktivesh  – Post doctoral fellow

Dr Matt Sinnott  – Principal Research Scientist

Dr Shourya Ghosh – Post doctoral fellow

Dr Simon Harrison – Principal Research Scientist

Dr Paul Cleary – Chief Research Scientist