UC Santa Barbara

Microbiota in the digestive tracts of herbivores are complex, highly-structured communities that degrade lignocellulosic biomass into simple sugars and then metabolize it into fatty acids, gases, and other small molecules, approximately three times as efficiently as the most advanced human-engineered processes in use (Godon et al., 2013). The degradative power of these communities arises from partnerships between organisms carrying out complementary metabolic tasks, which together constitute the processes of anaerobic digestion. Cooperative strategies arising from these partnerships that microbiota deploy during anaerobic digestion of complex substrates are not well understood. A fuller understanding of these strategies will shed light on underlying factors driving the division of labor at each stage of lignocellulolysis and aid in identifying genomic and transcriptional mechanisms that predict patterns of labor division in a given consortium. Applying this knowledge will enable the development of approaches to modulate the activity of existing microbiota and construct synthetic consortia to optimally transform complex substrates into desired products.In this body of work, we examine microbial relationships and consequent digestive strategies in the degradation of complex biomass as they manifest through both composition and activity, through employing enrichment to study the gut microbiota of captive individuals of three herbivore species – the San Clemente Island goat (Capra hircus), a foregut-fermenting hoofed mammal, the Eastern black and white colobus monkey (Colobus guereza), a foregut-fermenting primate, and the Western lowland gorilla (Gorilla gorilla gorilla), a hindgut-fermenting primate. In the first of two studies, we enriched a goat fecal microbiome in parallel cultures on three lignocellulosic substrates and hemicellulose, and then sequenced the actively transcribed genes from the microbes enriched on each substrate. We demonstrated that parallel enrichment on complex biomass subsrates and purified hemicellulose enriches consortia whose transcriptional activity is shaped by the substrate. However, this activity was likely limited by genetically-encoded factors inherent to the consortium. We also observed a previously-uncharacterized strategy for division of carbohydrate-active enzyme expression labor exhibited across all lignocellulosic substrates. We then investigated the composition and structure of lignocellulolytic communities in C. guereza and G. gorilla gorilla fecal microbiota, and attempted to enrich anaerobic fungi of the phylum Neocallimastigomycota from fecal samples of captive C. guereza and G. gorilla gorilla. This attempt was unsuccessful at enriching anaerobic fungi, but instead enriched a diverse community of other fungal taxa with diverse roles in lignocellulolysis, metabolism, and regulation of the microbial community and its host. We found that the C. guereza and G. gorilla gorilla gut microbiome contain rare bacterial and fungal taxa that may have important roles in lignocellulolysis in the gut, and that enrichment on complex substrates with the aid of antibiotics is an underutilized but crucial method for fully characterizing the diversity of herbivore gut microbiota by enabling the growth and sequencing of rare taxa in the microbiome. Taken together, these studies investigate relationships between microbes in lignocellulolytic gut consortia, through the lenses of community composition and activity, to yield new insights about how these consortia work together.