Biology Ph.D. Dissertations

Genome-Scale Metabolic Network Reconstruction of Thermotoga sp. Strain RQ7

Date of Award


Document Type


Degree Name

Doctor of Philosophy (Ph.D.)


Biological Sciences

First Advisor

Zhaohui Xu (Advisor)

Second Advisor

Yuning Fu (Other)

Third Advisor

Paul F. Morris (Committee Member)

Fourth Advisor

Vipaporn Phuntumart (Committee Member)

Fifth Advisor

Junfeng Shang (Committee Member)


Thermotoga are anaerobic hyperthermophiles that have a deep lineage to the last universal ancestor and produce biological hydrogen gas accompanying cell growth. In recent years, systems level approaches have been used to elucidate their metabolic capacities, by integrating mathematical modeling and experimental results. To assist biochemical engineering studies of T. sp. strain RQ7, this work aims at building a metabolic model of the bacterium that quantitatively simulates its metabolism at the genome scale. The constructed model, RQ7_iJG408, consists of 408 genes, 692 reactions, and 538 metabolites. Constraint-based flux balance analyses were used to simulate cell growth in both complex and defined media. Quantitative comparison of the predicted and measured growth rates resulted in good agreements. This model serves as a foundation for an integrated biochemical description of T. sp. strain RQ7. It is a useful tool in designing growth media, identifying metabolic engineering strategies, and exploiting physiological potentials of this biotechnologically significant organism.