I have been on 200mg per day for 7 months! Seems too long for an...

I have been on 200mg per day for 7 months! Seems too long for anyone to be on an antibiotic, since antibiotics can deteriorate your gut and colon. However, I suffer from pemphigus vulgaris, which is an autoimmune blister disease, whereby the body no longer recognizes the skin as part of self and attacks it as an invader. The doxy will make me severely nauseous without food. I have experienced the burning from the inside out, tingling and new blisters from the sun because of the doxy. It has been a long run, I imagine the anxious, depressed emotions could be from the doxy, however I am unsure. Always feeling tired has been quite common. I tried to stop, especially if I were going to be in the sun, but the consequences were severe with new sores appearing from my pemphigus. So in my case apparently the benefit outweighs the risk, for now. I have noticed in my 6 month that my knees and hips are in pain. Is that a side effect of long term use of this medicine? Not that may be worthy of reconsideration, if it is responsible for joint and bone deterioration.