Garret Suen

Microbial communities associated with herbivores are fundamental to ecosystem functioning in almost all environments on Earth. Specifically, these communities facilitate the conversion of plant biomass into nutrients usable by their host, thereby bridging primary producers and secondary consumers. My research is focused on understanding the evolution and ecology of herbivore-associated microbial communities on three different scales. At the broadest scale, I am interested in how these communities evolve across host type, host diet, and geographical distribution. At an intermediate level, I am interested in how members of these communities interact with each other to coordinate the breakdown of plant biomass and produce nutrients for their host. At the finest scale, I am interested in understanding how microbes fundamentally degrade polysaccharides (cellulose and hemicelluloses) in plant cell walls. My work can be applied to two specific fields as described below.

Biofuels. A major global challenge is to reduce our reliance on fossil fuels. Biofuels have been proposed as an alternative fuel source because of their cleanliness and sustainability. One proposed biofuel is cellulosic ethanol, which can supplement gasoline and integrate with our current transportation infrastructure. The generation of cellulosic ethanol requires the conversion of cellulose into simple sugars followed by fermentation into ethanol. My work directly impacts the first bottleneck of cellulose degradation. I use as a model system, ruminants, which are arguably one of the most efficient natural cellulose-degrading systems. Ruminants such as domesticated cattle harbor a specialized community of plant-degrading bacteria that ferment cellulose and other polysaccharides into small chain fatty acids. We are attempting to understand this process at a base level by characterizing the mechanisms through which ruminal bacteria like Fibrobacter succinogenes S85 and Ruminococcus albus 7 degrade cellulose. In particular, Ruminococcus albus 7 is capable of fermenting ethanol using cellulose in vitro. This work incorporates whole-genome sequencing, transcript sequencing using RNA-seq, prediction of protein-protein interactions using functional genomics, and in vitro cell-free expression of cellulolytic enzymes. Finally, these bacteria are known to work with other hemicellulolytic ruminal bacteria to synergistically enhance their overall cellulolytic and fermentative abilities. We are also investigating these interactions to gain an understanding of this process.

Animal Health and Production. Ruminants are major agricultural resources, particularly for the production of products like beef and milk. Milk production is linked to the ruminal microbial community, as the small chain fatty acids produced by these microbes directly impacts the quality of milk produced by cows. We are interested in understanding the ecology and evolution of these ruminal communities and their impact on milk production. Specifically, we are working to understand the confluence of diet, host genotype, and ruminal microbiota on milk quality. We use a combination of metagenomics, metatranscriptomics, milk production metrics, and cow health to assess these factors. We are also interested in understanding how rumen microbiota become established in developing calves, and in particular, how diet influences microbial composition. Finally, these studies have direct impact on human health and disease, particularly in development, lactation, and the influence of diet on host microbiota. Ruminants are excellent models for understanding these factors in humans as they share a large number of genes, can be directly manipulated at the ruminal level, and can be reared on controlled diets.