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1 If the liver is unable to break down the ammonia it is excreted in the urine.  Other diseases - Other common causes of the ammonia smell in urine are diabetes, metabolic disorders, sexually transmitted diseases, medications, vitamins, and nutritional supplements.
Mammals metabolize ammonia into a molecule called urea: As you can see, this molecule contains two atoms of nitrogen. Although it requires metabolic energy to build, it also is less toxic than ammonia, and it requires less water to flush from the system.Your urine's main nitrogenous waste product is urea.itrogen combines with other molecules in the body to produce toxic compounds such as ammonia. And so the animal must find a way to excrete these toxins. As we already know, this is the function of the kidneys and the rest of the renal system. Ammonia has only one nitrogen per molecule, but it is quite toxic.