(191dd) Systems Biology Analysis of Natural Biomass Utilization Microbiomes for Biotechnology Applications

Many natural biomass utilization systems (NBUS) can efficiently degrade ligocellulosics. Typical NBUS include microbiomes for efficient biomass degradation, such as the microbiota in bovine rumen and herbivorous insect guts. We have carried out comparative systems biology analysis of multiple microbiome systems in insect guts and cattle rumen. Metagenome analysis of the gut symbionts of three different insects specialize on different food types was conducted as a means of comparing taxonomic and metabolic diversity of gut microbiomes to diet and life history of the insect hosts. A second goal was the discovery of novel biocatalysts for biorefinery applications. The comparative analysis revealed dramatic differences among the three insect species in the abundance and taxonomic composition of the symbiont populations present in the gut. The composition and abundance of symbionts was correlated with their previously identified capacity to degrade and utilize the different types of food consumed by their hosts. The metabolic reconstruction revealed that the gut metabolome of cutworms and grasshoppers was more enriched for genes involved in carbohydrate metabolism and transport than wood-feeding termite, whereas the termite gut metabolome was enriched for glycosyl hydrolase (GH) enzymes relevant to lignocellulosic biomass degradation. Moreover, we cloned and further characterized multiple biomass-degrading enzymes and established that the grasshopper symbiont enzymes were generally more efficient in biomass degradation than the homologous enzymes from cutworm symbionts. Together, these results demonstrated a correlation between the composition and putative metabolic functionality of the gut microbiome and host diet, and suggested that this relationship could be exploited for the discovery of symbionts and biocatalysts useful for biorefinery applications. In addition to insect guts, we have carried out comprehensive proteomics analysis of microbiomes in cattle rumen to study the molecular mechanisms of biomass deconstruction and utilization. We have included four treatments of high fiber, low fiber and medium fiber diet in the treatments in a 72 day feeding trial. Metagenome sequencing was first carried out to derive the gene models for proteomics data search. Enzyme assays revealed that the cellulytic enzyme activities are higher in the high fiber biomass treated time point. MudPIT-based shot-gun proteomics was carried out to characterize both the soluble and fiber portion of the rumen material. The proteome profiling highlighted that microbial diversity and enzyme profile change dramatically in response to the feeding content. Furthermore, cluster analysis and protein co-regulatory network modeling of protein abundance revealed that several groups of enzymes are coordinatively regulated in response to the high fiber biomass feeding. Each group of these coordinative enzymes includes multiple glycoside hydrolase (GH) families and functional category, indicating the synergistics toward biomass deconstruction. More importantly, the protein profiling correlates with the metagenome analysis in a way that some co-regulating enzymes were found in the same operon in metagneome sequences. The results highlighted both the regulation mechanisms and the reliability of proteomics data. Based on the network modeling, we have cloned and characterized multiple enzymes toward reverse design of a biorefinery process for efficient biomass utilization. Overall, the systems biology analysis revealed the potential mechanisms for efficient biomass degradation in various biomass-degrading microbiota, which can be used to guide the enzyme discovery and biorefinery design.