It is believed that arginine is utilized during the replication of viruses and protozoans (I don't believe that but it's just semantics) and in chronic cases of diseases from them, your arginine level can get low. If you analyze the foods that you really like to eat and examine what they are made of, you can see how much arginine is in them.
Arginine is a protein that we eat and it is converted to ornithine during the urea cycle (the cycle that helps us get rid of nitrogen). Ornithine is then converted into putresine which is a polyamine. It is my belief that the polyamines are the major problem for chronic Lyme patients. They are essential and very important for many cellular functions. When their numbers start decreasing inside our cells, we start aging and having problems.
When people start to have a bad body odor or smell funny, this is the cycle that is not functioning properly.
Even though arginine is converted to ornithine, this (like many pathways) can go back words and under certain conditions, ornithine can be converted back to arginine. There is a proper ratio between the two and the pathway needs to go forward, not backward. Problems with arginase or the enzymes between the two can cause a backward direction provided the pH of the cytoplasm is conducive for this. Experimenting with what you eat can sometimes help determine what is going on in this pathway.
Here's an example of the pathway, just look at the pics if the terminology is more than you want. Note where collagen synthesis is located. All of these pathways are intertwined and lysyl oxidase deficiency can be just part of the problem if the pathway isn't functioning properly.ccforum.biomedcentral.com/articles/10.1186/cc11205
Protozoans can sometimes mimic enzymes in this pathway to change the concentrations of vital components.