Significant metabolic interactions exist between the gut microbiota and the mammalian host, one prime example of which is nitrogen metabolism. In the colon, bacterial urease hydrolyzes host-derived urea into carbon dioxide and ammonia. Colonic ammonia can subsequently be absorbed by the host or utilized by the gut microbiota for additional nitrogen metabolism. In patients with liver disease such as cirrhosis and congenital urea cycle disorders, hepatic abnormalities prevent the normal processing of ammonia, leading to hyperammonemia and hepatic encephalopathy (HE). Although circulating ammonia levels are correlated with damage to the central nervous system, the pathogenesis of HE is complex and not fully elucidated, hindering progress in treatment. Current treatment options including antibiotics, lactulose, and a low protein diet (LPD) are complicated by issues such as side effects, concerns of safety and efficacy in long-term use, and poor adherence. Our goal is to develop a safe, durable, and efficacious treatment for HE through the inoculation of a urease-free bacterial consortium. We show that we are able to engineer the gut microbiota to reduce fecal urease activity and ammonia levels in mice. Depletion of the endogenous gut microbiota followed by transplantation with Altered Schaedler Flora (ASF), a defined consortium of eight murine gut commensal bacteria with minimal urease gene content, established a persistent new community that exhibited long-term reduction in fecal urease activity and fecal ammonia production. ASF transplantation was associated with a decrease in morbidity and mortality in the thioacetamide (TAA) murine model of hepatic injury and fibrosis. Although the ASF consortium demonstrated reduced resilience in response to dietary stress, ASF transplantation led to further reductions in fecal ammonia on a LPD without exacerbating host metabolic dysfunction. These findings point to the potential use of a human urease-free bacterial consortium to alter clinical management and outcome in HE. Furthermore, they provide proof of concept that microbiota transplantation with a defined microbial consortium can lead to durable metabolic changes with therapeutic utility.