Anaerobic Microbial Consortia Omics to Design Agile and Expedient Bioreactors

To win in the deep operational environment, the Army will need to be more adaptive and expeditionary with less logistic demand. Readily available resources such as food waste and vegetation provide waste streams from which to generate energy and materials at the point of need. These substrates are poor candidates for chemical conversion; however, microbes such as the inhabitants of human and ruminant guts can ferment these waste streams to commodity/specialty chemicals. Industrial fermentations using these microbes generally involve monocultures with highly controlled conditions that are inflexible to changing waste streams and environmental conditions. We propose to overcome these challenges with reconfigurable microbial reactors that customize consortia composition to direct variable waste inputs to tunable products. We hypothesize that consortia will outperform monocultures for waste to chemical production in Army relevant conditions. To assess consortia vs monocultures for chemical production from lignocellulosic feedstocks, we experimentally combined ruminant gut fungi with Clostridium acetobutylicum (Cac). The fungi degrade lignocellulose to release carbohydrates that Cac then converts to useful chemicals. This carbohydrate mixture contains substrates with varying redox states known to affect Cac metabolic outputs. We further characterized the transcriptome and proteome of Cac in the presence of these substrates in order to understand their effects on metabolic regulation. The data was incorporated into a genome-scale metabolic model to better predict metabolic outputs and understand how genetic manipulations could direct useful chemical production given variable substrate inputs. Thus, we provide a theoretical and experimental framework to design, test, and build functional microbial consortia for expeditionary force sustainment.