image: New project, MATOMIC, will investigate the role of gut microbiomes in obesity. view more
Credit: MATOMIC/University of Southern Denmark
The human gut is inhabited by more than 1,000 different species of microorganisms, primarily bacteria. The vast majority are beneficial and harmless, but in recent years, researchers have discovered that the intestinal microbiome is altered in obese patients.
Consequently, there is scientific and medical interest in trying to reverse the microbiome of the obese, for example via fecal transplants, in which obese patients receive intestinal bacteria from a normal-weight donor.
- Some 10 years ago it became clear that it works. But how? What exactly is going on? We don’t know. If we are to find the best treatments, we will need to know in detail what goes on in the microbiome of the intestinal system and how it responds to treatment,” said Daniel Merkle.
He is a Professor at the Department of Mathematics and Computer Science, University of Southern Denmark, and coordinator of the new research project, MATOMIC, which will develop mathematical models of how intestinal bacteria influence our health.
Computational chemistry
Traditionally, chemists work in a laboratory, but when it comes to finding answers to the very large and complex chemical questions such as: How did the first life forms on earth arise? or: How do cells work in humans, at the chemical level? Computer models can be a great help.
Examining an entire microbiome is a physically and practically impossible task - understood in the sense that no laboratory methods can simultaneously measure all the interactions that take place between individual enzymes, proteins and molecules in every bacterium found in a person’s microbiome.
As mentioned before, more than 1,000 different species live here, and in total there are more than 100,000,000,000,000,000 individual microorganisms in a human intestinal system.
Mapping all the possible chemical reactions
Where laboratory methods fall short, mathematics and computer science will contribute, and this is the plan for MATOMIC.
- We are interested in mapping all the possible chemical reactions, interactions and networks that may occur among these actors. Some reactions support others, some reactions inhibit others. The possible number of interactions is very large,” said Rolf Fagerberg, who is a professor at the Department of Mathematics and Computer Science and part of the project.
What happens at the atomic level?
- We want to create mathematical models and simulations of what goes on in the intestinal system - all the way down to the atomic level,” said Jakob Lykke Andersen, associate professor at the Department of Mathematics and Computer Science and also part of the project.
The team is now in the process of developing new algorithms and other tools for a new toolbox, that will allow researchers to create a virtual gut system where chemical reactions and networks can be tested. Chemists and biochemists participating in MATOMIC will contribute to the development and verification of the virtual models.
The project is scheduled to end with mouse trials - and if successful, they could pave the way for clinical trials on humans.
MATOMIC (Mathematical Modeling for Microbial Community Induced Metabolic Diseases) employs 15 researchers over six years and is supported by the Novo Nordisk Foundation. https://www.sdu.dk/en/forskning/matomic.