Thought I'd give a preliminary look at some of the stuff I'm currently looking into.
There are 4 phyla of bacteria in the GI tract. No names today but one phylum of bacteria produce tryptophanase. This is the enzyme responsible for breaking down tryptophan. This is a problem many Lyme patients experience, a reduction in tryptophan levels and the problems that may follow like anxiety, insomnia, hypertension, depression, etc.
Tryptophanase takes tryptophan and water to form indole, pyruvate, and ammonia. This is not good. This enzyme also helps with nitrogen metabolism so eating animal protein can increase its levels and can be problematic for most people with Lyme Disease. it has Vit B6 and potassium as cofactors in its reaction.
If one has adequate lactobacillus and clostridium spongene levels, then tryptophan is broken down into neuroprotective agents and antibiotic-like substances. Wouldn't this be great?
Without going too much further, the difference in being healthy verses being unhealthy could simply be your bacterial assortment and concentrations. I'm getting some wild ideas why this is the case.
Key players here: Vitamin B6, Water, Manganese, Potassium, Tryptophan, Vitamin D, Vitamin B12, Niacin, Pantothenic Acid, pH, and Nitrogen. I'm sure there are more.