Are there known drawbacks of long-term doxycycline use against acne? excluding changes to endogenous microbes and sun sensitivity.

Not really: Doxycycline as generally all tetracyclines are fairly well tolerated in patients with long term use. I have patients who've taken them over a long period of time without major side effects.

Possibly predispose.: Generally, i recommend discontinuing oral antibiotics after 9-12 months. Beware of possibility of developing other acne like breakouts such as pityrosporum folliculitis, which tends to be itchy and can be associated with long term antibiotic use. Also, may develop pseudomonas acne which is a bacteria that is often found in loofas and other wet scrub type brushes.