Final Report Summary - MICRODE (Interpreting the irrecoverable microbiota in digestive ecosystems)
The MicroDE project utilized recent advancements in molecular and computational technologies to study vital pieces of genetic information from microbes that cannot be grown in the lab (as well as those that can). Specifically, this process included recovering the microbes genes and then using this data to re-create the enzymes that perform their important tasks. Using this toolkit, we focused on important fiber-degrading microbes found in wide reaching environments, such as the gut of humans as well as domestic and wild animals (e.g. cows, pigs, fish, moose), soils and industrial reactors that convert waste to biofuel. These approaches revealed new microbes that have not been encountered before in nature, and discovered that they use complex enzymes that are different from those previously known to scientists. Excitingly, we also discovered that viruses in soil possibly utilize plant biomass-digesting enzymes, and that several well-known microbes produce small spherical buds (known as outer membrane vesicles), which are released from the host microbe and are highly capable of digesting plant biomass. We have also shown that horizontal gene transfer (HGT) plays a significant role in dictating plant biomass conversion in some biofuel-creating microbiomes, by revealing that key protein-degrading microbes that are known to numerically dominate industrial biogas plants have evolved via HGT to a plant biomass-degrading lifestyle. Finally, our detailed analysis of individual plant-biomass digesting microbes as well as complex animal-associated microbiomes in “real-time” has generated deeper understanding into the different enzymatic tools and intricate microbe-microbe networks that occur in microbiomes that perform in situ plant fiber deconstruction. This knowledge is helping improve our understanding of nutrition in important production animals and actively enabling scientists to design novel feeding strategies that are currently being implemented in key animal systems.