Metabolic Engineering of Seaweed Polysaccharides in Therapeutic Human Gut Microbes

Probiotic bacteria often struggle to effectively colonize the human gut when administered as a medical intervention. Studies have shown that a predictive factor for whether a probiotic bacterial species will be able to effectively colonize a gut is whether or not it can occupy a carbon-utilization niche that is not already taken by a preexisting species. The carbohydrates porphyran and agarose found in red seaweed, such as nori, represents such a unique carbon source that is largely absent from the western diet. Research has shown that the colonization of porphyran-digesting gut microbes can be finely controlled by feeding porphyran to the host animal. This ability to tune and control colonization of the gut microbiome by engineering a synthetic metabolic niche could be broadly useful for many medical applications utilizing therapeutic gut bacteria to increase the efficacy and affordability of these treatments.

The aim of this project is to elucidate how the porphyran or agarose utilization metabolic pathway can be transferred to a phylogenetically distant gut microbe that is used therapeutically. A goal is to engineer Escherichia coli to digest and utilize the carbohydrates found in red seaweed and engineer its ability to colonize the gut. E. coli is an easily cultured and genetically tractable model organism. Our approach is to engineer E. coli to metabolize porphyran or agarose by expressing and secreting novel porphyranase and agarase enzymes from seaweed-degrading bacteria, such as Bacteroides plebeius. We will express the enzymes and modulate expression of native metabolism genes in order to optimize E. coli for porphyran or agarose degradation. This optimization will be informed by genome-scale metabolic modeling and flux balance analysis.