Hmmm, Rockt. You ask good questions, which I will try to answer. Now that I really think back, I have been on doxycycline for almost ten years*. But, have I really? When I started, I was terrified of my possible reaction so I opened up a capsule, removed a speck of the powder and took that. It absolutely knocked me off my feet - I had a huge increase in chemical sensitivity for a day or so, then back to baseline. Over the years I slowly increased my dose (I used a balance in a research lab). And, over these years, I have become less chemically sensitive.
When I first started doxy, I couldn't even go to the lab to measure out my doses due to chemical exposures. Now, I am able to work part time in a very demanding, intellectually challenging job. The other thing that had to change in order to work outside the home was my level of weakness and fatigue. I'm not sure that doxy ever touched that, to be honest. But, undergoing chemotherapy for cancer DID have a dramatic effect. In a few days I was able to go for walks (first time in YEARS).
I am fairly comfortable with my fatigue component of this disease now.....but the chemical sensitivity is what is preventing me from moving forward. I think the methylation supplements have had a big effect, but for some reason, seem to have made me more chemically sensitive.
Regarding concerns of damage to the gut, I should also say that when I was extremely chemically sensitive, I could only eat a few foods as well, so lots of food sensitivities too. THese have improved too; I suspect that doxy has been the help here. Now I can get away with eating almost anything, at least for a short time. Before I wasn't even tempted to cheat since the reactions were so intense.
My belief is that there is a genetic component for all this....I had a relative who had severe MCS too, and I don't think it's because both of us had lyme. Doxycycline also modulates the immune system and I think that this is why it's helpful. I could be wrong, and I guess shortly I may find out. My doctor wants to take me off doxy and try another antibiotic. I dread this. I want to keep my job. I worry that if my chemical sensitivities get stirred up even more I won't even be able to do part time.
I am still not at the therapeutic dose of doxy, but the way. I'm about halfway there. I can't even imagine the level of hell that may have ensued had I started out at the full dose. *cringe*
I hope this helps.