this is a good question.
Ammonia is a product of protein digestion, so low protein diet is usually prescribed to people with hepatic encephalopathy, but antibiotics is also given to these people when they have crisis, so gut microflora may produce more NH3 than our own body from proteins catablism.
This is something to dig into!
Ammonia level may be even more important to control if thyroid hormons are involved in our illness, because NH3 seems to be a T3 antagonist:
"One of the TR antagonists evaluated in animal studies is NH3. NH3 is a TR inhibitor[
64,
67]
in vitro and
in vivo in amphibians, although some partial agonist properties were seen at higher doses. In rats, NH3 showed TR inhibition that increases up to the 924 nmol/kg/day dose, and there was a loss of these effects at higher concentrations. At high doses, it showed apparent partial agonistic activity for cholesterol, heart rate and TSH. NH3 is not TR subtype-selective
in vitro, and it does not seem to be selective in rats, because both TR α- and TR β-mediated parameters were inhibited.[
62]
The exact reason for this loss of antagonistic activity at high doses is not known. It may be due to true partial agonist activity or a metabolite with agonist properties may be generating this. It is also possible that increasing TSH might also increase circulating THs and, at higher concentrations, the higher levels of T4 and T3 could surmount the NH3 antagonist effects.[
62]
Pharmacology of NH3 action is complicated. It requires almost 1 week to develop both agonistic action at low doses and antagonistic action at high doses. Although NH3 had no effect on TSH at either dose, it lowered cholesterol to equivalent levels at both doses, despite the great difference in the doses. Hence, it is stated that at least several days of treatment are necessary for TR antagonist effects to become apparent.[
62] Therefore, if NH3 is to be evaluated in humans in the future, it should be used with caution and in proper doses."
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3683193/
