Engineering Microbial Communities

“Microbes have friends, enemies, and ‘frenemies’,” Michelle O’Malley tells us. O’Malley, a researcher at UC-Santa Barbara, is interested in engineering the rumen microbiome to better turn plant waste into something valuable. Lignin, a plant material that is particularly difficult to break down, is one of O’Malley’s targets. Anaerobic consortia in cattle rumens are already highly effective at breaking down many resistant types of biomass, and these microbe communities could provide solutions for the breakdown of a variety of resistant materials. O’Malley’s lab seeks to learn from nature to build stable anaerobic consortia with novel functions to accelerate getting renewable fuels and useful materials from waste products.

“Communities are more creative and productive than individuals,” says O’Malley, emphasizing that many microbes share and exchange metabolic byproducts. Anaerobic fungi are powerful crude biomass degraders, good at “punching into” plant biomass and starting to break it down. They possess more biomass-degrading enzymes than any other groups found to date. These gut fungi had received little attention for some time because they had not been isolated from microbial communities.

Using microbial lines from animals ranging from cattle to horses to elephants, O’Malley’s lab is working to create synthetic microbial communities that might never assemble in nature, but can still meet each other’s needs as a community. These synthetic communities have remained functional for a week or more, but then fall apart for reasons that remain unknown, perhaps duet to secondary metabolites secreted by the organisms. Understanding the partnerships between fungi, bacteria, and archaea makes it possible to engineer novel, stable microbial consortia that could serve engineering needs.