Anaerobic microbes evolved to work together in complex communities that decompose and recycle carbon biomass throughout the Earth – from our guts to landfills and compost piles. Compared to microbes that thrive in the presence of oxygen, anaerobes are woefully understudied and are recalcitrant to culture; they represent a vast, untapped resource for novel enzymes that degrade woody biomass into sugars, as well as natural products that could find use as new drugs. Despite their importance, little information exists to parse the role of each microbial member within their dynamic community.<br/> <br/>To address these knowledge gaps, we pioneered new techniques to isolate anaerobes from biomass-rich environments (e.g. guts and fecal materials of herbivores) and build synthetic consortia to uncover their interdependencies. Initially, we tracked the development of enrichment cultures from goat fecal pellets grown on four types of substrates: alfalfa stem, bagasse, reed canary grass, and xylan over several generations. We tested the hypothesis that the composition of these enriched consortia would stabilize to match the metabolic requirements needed to degrade each substrate. Metagenomic sequencing of the 16S rRNA (prokaryotes), 18S rRNA (eukaryotes), and ITS (fungi) population within the consortia revealed strong specialization of the microbes during selection, suggesting that the membership of each culture tuned to match the substrate. Using these natural systems as inspiration, synthetic consortia of fungi, bacteria, and methanogens were combined in culture and tested for stability and substrate hydrolysis. In nearly all cases, synthetic consortia demonstrated faster and more complete degradation of cellulosic substrates, as well as a wider range of utilized substrates compared to monocultures. We will further discuss the roles that interwoven metabolism and secondary metabolites play on microbial consortia dynamics, both in natural and synthetic systems. Overall, the stable microbial consortia we identified here directed the formation of synthetic, interdependent communities via a bottom up approach to compartmentalize biomass-degradation and bioproduct formation.<br/>

Engineering synthetic consortia inspired by the rumen microbiome

255th National Meeting (2018)

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