Gut bacteria produce GABA.  I've been teaching biochemistry for over 20
years to medical students and I've always told students that brain
involvement in patients in terminal liver failure was due to ammonia load
as well as D-amino acids that the liver can't take out.  Our new textbook
pointed out that gut bacterial production of GABA was also a major factor
in coma and brain death in patients with liver failure.  Gut and liver are
supposed to take out all glutamate and aspartate that comes from the gut
(some of it bacterial produced).  Both aspartate and glutamate function as
neurotransmitters in humans.  When liver function is low, some aspartate
and glutamate could escape and end up affecting brain function.  High
producing GABA, aspartate and glutamate strains of bacteria in the gut
could affect brain function.  I've not seen any proof that in patients with
normal gut and liver function that gut bacteria can impact brain function
though.

Pyotr The Great ?

Several potential biogenic amines may be produced during the metabolism
of nitrogenous materials in the colon, eg  octopamine, tyramine,
Histamine, etc. Short chain fatty acids (Butyrate) and metabolism of some
sulfur-containing amino acids may also have neurologic effects.  Steven
Schenker had papers about this about 20 years ago and the basic
principles are used to some degree in the management of patients with
hepatic encephalopathy.  

(Plain ol') Pete