Hao Luo, Systems & Synthetic Biology
"Modeling human gut microbiota: from steady states to dynamic systems"
Opponent: Associate Professor Vassily Hatzimanikatis, École Polytechnique Fédérale de Lausanne, Switzerland
Supervisor: Professor Jens Nielsen, Chalmers
Examiner: Research professor Verena Siewers, Chalmers
Do you know how many gut microbes are in your body? Their cell numbers are close to the number of our human cells. The human microbiota is not only huge in number but also diverse. There are probably more than 2,000 different species of bacteria, viruses, fungi, and other microbes in our gut. They have 100 times more genes than those in the human genome. Are you as curious as I and my collaborators are about what they are doing in our bodies and how they affect our health? In this thesis, I have used genome-scale metabolic models (GEM) to create a "map" of gut microbiota metabolism. This "map" provides insight into the behavior of microorganisms and the metabolic potential at a steady state. In addition, I used cybernetic models to illustrate the "traffic conditions" and resource allocation in this "map", simulating the dynamic behavior of human microbiota.
The importance of the gut microbiome for bone metabolism and T2D has been demonstrated in mice and human cohorts. To study this, a GEM for Limosilactobacillus reuteri ATCC PTA 6475 was reconstructed, this probiotic bacterium significantly reducing bone loss in older women with lower bone mineral density. To investigate the associations between T2D and the gut microbiota, GEMs for T2D cohorts have also been constructed. Furthermore, integrating the models with the machine learning method provides potential insight into the possible roles of gut microbiota in T2D. The remaining part of this thesis focuses on using cybernetic models to explore human gut microbiota interactions and population dynamics. Together with my collaborators, I have developed a computing-efficient strategy for model reconstruction and simulation to reveal the metabolic dynamics of human gut microbiota.
In this thesis, I have explored the human gut microbiota from single L. reuteri species to microbial gut communities, from simple steady-state systems by GEMs to complex dynamic systems by cybernetic model.
10:an, meeting room, Kemigården 4, Kemi & via Zoom
07 November, 2022, 13:30
07 November, 2022, 16:30