In silico analysis of microbial communities through constraint-based metabolic modelling
Doctoral thesis, 2019
GEMs are powerful tools to model an organism’s metabolic capabilities, and although numerous GEMs have been reconstructed, their quality control has not gained enough attention. Evaluation of a repository of semi-automatically reconstructed GEMs related to the human gut microbiota and another repository of manually curated ones was performed comparatively. Assessing these models from topological and functional aspects, it was shown that semi-automatically reconstructed models required extensive manual curation before they could be used for target-specific simulations.
In constraint-based modelling, an objective function is usually optimised under particular environmental conditions, however, in case of the microbial communities, there is no distinct and relevant objective function. Therefore, an unbiased uniform randomised sampling algorithm was implemented for microbial communities. The samples acquired from the solution space were analysed statistically to see clustering patterns of the reactions and commensalistic relationships between the community members were identified. Overall, computational modelling paves the way towards gaining a mechanistic understanding of microbial communities and provides us with testable hypotheses and insight.
fermented food production
genome-scale metabolic model
lactic acid bacteria
uniform randomised sampling
Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology
Gut microbiota dysbiosis is associated with malnutrition and reduced plasma amino acid levels: Lessons from genome-scale metabolic modeling
Metabolic Engineering,; Vol. 49(2018)p. 128-142
Challenges in modeling the human gut microbiome
Nature Biotechnology,; Vol. 36(2018)p. 682-686
Other text in scientific journal
Parizad Babaei, Christian Chervaux, Chloë Beal, Jean-Michel Faurie, and Jens Nielsen, Computational design of optimum bacterial consortia for milk fermentation using genome- scale metabolic models
Parizad Babaei, Promi Das, Adil Mardinoglu, and Jens Nielsen, Uniform randomised sampling of microbial communities
Promi Das, Parizad Babaei, and Jens Nielsen, Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome
Human gut microbiota and healthy aging: Recent developments and future prospective
Nutrition and healthy aging,; Vol. 4(2016)p. 3-16
Bioinformatics (Computational Biology)
Bioinformatics and Systems Biology
Doktorsavhandlingar vid Chalmers tekniska högskola. Ny serie: 4557
KA-salen. Kemigården 4, Chalmers.
Opponent: Bas Teusink