Engineering E. coli Nissle to Degrade Toxic Compounds in Mouse Models of Metabolic Disease

The complex communities of microbes that live within the human gastrointestinal (GI) tract greatly impact human health through metabolic processes, their interactions with each other, and their interactions with the immune system. When functioning in concert with their hosts, the gut microbiota can supply nutrients, degrade toxic compounds, and prevent overstimulation of the immune system. The gut microbiota, as a whole, is so active that its combined metabolic output can be thought of as an additional organ. By manipulating these processes through genetic engineering, we can generate microbes that supply missing metabolites and degrade specific toxic compounds in order to relieve inborn metabolic disorders and supplement organ deficiencies.

Urea cycle disorders (UCD) are a collection of genetic conditions with an estimated incidence of 1:8,500 births, in which the patient is unable to convert nitrogen to urea, resulting in the toxic accumulation of ammonia systemically. This hyperammonemic state can lead to CNS impairment, affecting neurological function, impacting normal development and in some cases, can be fatal. Importantly, as much as 70% of excess ammonia in hyperammonemic patients accumulates in the GI tract, supporting the use of a modified gut microorganism-based therapeutic. We have engineered Nissle, a probiotic strain of E. coli, to reduce the concentration of blood ammonia in those suffering from hyperammonemia caused by UCD. Nissle has been modified to respond to the gut environment and activate a carefully optimized ammonia consumption pathway. Through in vivo studies, we have shown that our engineered Nissle strain can sequester the ammonia produced via digestion, thus preventing diffusion of ammonia into the blood. Lowering blood ammonia levels also decreased mouse mortality compared to controls. Our work demonstrates that engineered microbes can be introduced into the gut microbiota, sense their local environment in that compartment, and affect an intended response in order to treat metabolic disorders. This prototype provides a meaningful example of how the tools developed in synthetic biology can be translated into the clinic.