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Interpreting the irrecoverable microbiota in digestive ecosystems

Final Report Summary - MICRODE (Interpreting the irrecoverable microbiota in digestive ecosystems)

The actions of microbes are responsible for creating and recycling the vital building blocks that sustain all forms of life on earth. For example, the gastrointestinal tract (or gut) of all mammals depends on a vital relationship with a community of microbes such as bacteria, archaea, protozoa, fungi and viruses (collectively referred to as a “microbiome”), which control the conversion of ingested fiber into nutrients whilst forming a protective barrier against disease and infection. Microbes also play a central role in the turnover of carbon-rich organic biomass in other natural ecosystems (e.g. soil) or in the industrial production of bioenergy (e.g. biogas reactors). With the help of microbes, we can convert a wide range of plant biomass and agricultural waste into renewable fuels and bioproducts. The microbial degradation of organic matter is usually not carried out by one microbe, but rather complex microbiomes, wherein individual microbes produce molecules called enzymes, and work together with other microbes by performing different tasks that complement each other. Researchers who wish to study these important microbes and their enzymes, encounter many technical challenges. One key bottleneck is that the vast majority of microbes that exist in nature cannot be removed from their innate microbiome and grown and studied in isolation within the laboratory, which means a complete understanding of how they operate and collaborate is restricted.

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.