Compositions, e.g., pharmaceutical compositions, nutritional compositions, medical foods, and food ingredients, as well as their methods of use, are provided, for treating diseases associated with hyperammonemia, e.g., urea cycle disorders (UCD) and hepatic encephalopathy (HE), e.g., minimal HE (MHE) and overt HE (OHE), and modulating enzyme activities and levels of microbes and taxa, and metabolites (e.g., ammonia) in the microbiome of a subject.