Genome-Scale Metabolic Reconstruction and Analysis of a Pure Culture Anaerobic Digester Public Deposited

http://ir.library.oregonstate.edu/concern/graduate_thesis_or_dissertations/rx913s89c

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  • Anaerobic digestion is a biological process in which organic matter is decomposed by a community of microbes in the absence of oxygen. The end product of anaerobic digestion is biogas, composed of methane and carbon dioxide, which is often recovered and used to generate energy. Commonly, biogas is not produced in sufficient quantities suitable for economic recovery, resulting in the flaring of biogas to the atmosphere. To optimize anaerobic digestion performance, in silico models have been created. Current models examine the critical components of anaerobic digestion, approaching the system at a macroscopic level. To address the limits of current macroscopic in silico models, a genome-scale model (GEM) of a pure culture anaerobic digester was constructed to evaluate both the individual organism’s metabolic activity and the community level fitness. An in silico pure culture anaerobic digester GEM was defined to include the acidogenic bacteria Clostridium acetobutylicum (iCac802), the syntrophic short chain fatty acid oxidizer Syntrophomonas wolfei (iTK530), and the methanogenic archaea Methanosarcina barkeri (iMG746). While GEMs for both C. acetobutylicum and M. barkeri have been previously published, a novel GEM for S. wolfei ( iTK530) was curated. Flux balance analysis was performed on the S. wolfei GEM to determine reaction fluxes through the system for various experimental conditions. The pure culture anaerobic digester was analyzed through the application of OptCom and descriptive-OptCom, which utilized multi-level and multi-objective optimization techniques. The construction of a pure culture anaerobic digester GEM presents a high resolution platform for in silico analysis and continued investigation of anaerobic digestion at the genome level.
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