This article explains it quite well.
The presence of ammonia in the blood stream is exacerbated by inflammation, oxidation, and infection. Interestingly, emerging strategies against HE include N-acetylcholine (to rebuild glutathine as an antioxidant) and probiotics.
From the article:
"Modulation of intestinal microbiota is an emerging strategy to reduce the bacterial translocation of LPS and other bacterial activators of TLRs. Probiotics have been shown to reduce bacterial translocation and were shown to improve liver function and prevent the development of infection and HE in patients with cirrhosis[124]. Furthermore, probiotics have been shown to restore neutrophil phagocytic capacity in patients with alcoholic cirrhosis, possibly by reducing endogenous levels of IL-10 and TLR-4 expression[130]."
In the above paragraph, the term, "bacterial translocation" refers to leaky gut syndrome, or other situations where intestinal bacteria infect otherwise sterile parts of the body, such as the blood stream or organ tissues, resulting in bacteremia or septicemia.
http://www.wjgnet.com/1007-9327/16/3347.asp
its a condition known as encephalopathy - if its due to a cirrhotic liver its referred to as hepatic encephalopathy - when the liver is unable to function normally - it cant properly break down proteins all the way - the result is a build up of ammonia in the system - this impairs cognitive function - also referred to as brain fog
In the context of advanced liver disease, elevated serum ammonia is often a product of protein metabolism, or the lack of it. Protein, and particularly meat protein produces ammonia in the colon; and while a healthy liver can manage this, a cirrhotic liver is often incapable of removing it.
This results in ‘brain fog’, or hepatic encephalopathy. It can often be effectively managed with the drug ‘Lactulose’; a laxative that encourages frequent bowel movements. Another drug, Rifaximin, an antibiotic has been used recently as well; you can discuss all this with your doctor, assuming it’s you that is dealing with this issue.
--Bill