(404d) Area 15C Plenary Award - from Trash to Treasure: Bioprospecting Nature’s Microbial Communities for Biotechnology

Anaerobic microbes work together in complex communities that decompose and recycle carbon biomass throughout the Earth – from our guts to landfills and compost piles. Despite their importance, little information exists to parse the role of each microbial member within their dynamic community. Even though sequencing provides clues to how microbes interact, we still lack the ability to cultivate “unusual” microbes to learn nature’s design rules. To address this knowledge gap, we pioneered new techniques to isolate anaerobes from biomass-rich environments (e.g. guts and fecal materials of herbivores), characterize their shared metabolism, and build synthetic microbiomes to drive biomass to renewable chemicals and materials. Specifically, we focused on preserving the microbial diversity of anaerobic gut systems, which enabled cultivation of rare members of the microbiome (e.g. fungi, archaea) that play a key role in degradative function. Along with a wealth of carbohydrate active enzymes, we also uncovered a plethora of gene clusters encoding biosynthetic enzymes for secondary metabolites from diverse chemical classes by mining the genomes and transcriptomes across the anaerobic gut fungi (Neocallimastogomycetes). Key secondary metabolite clusters include those that build polyketides and non-ribosomal peptides, and several of these clusters appear to be horizontally transferred from anaerobic bacteria. Overall, our analysis points to natural compartmentalization between anaerobes as a means to degrade crude biomass, which can be exploited to harness nature’s microbes for sustainable chemical production using synthetic systems. For example, by combining anaerobic fungi with chain elongating anaerobic bacteria in synthetic co-culture, we established a cross-feeding system that enables production of short and medium-chain fatty acids directly from lignocellulose. Using analogous bioprospecting approaches, we are currently selecting for plastic-degrading microbial communities in the herbivore rumen, as well as in the natural oil seeps of the Santa Barbara Channel.