My periodontist said i can take periostat (doxycycline) indefinitely. is this true, or is there a danger with constantly taking it (as it could kill good bacteria)?

Low dose not harmful: Periostat is a low dose of the antibiotic doxycycline found to be helpful with adult periodontitis. At this dose the effect on mouth bacteria is minimal. It is a medication often prescribed at a much higher dose for long term control of acne. The biggest concern would be pregnancy which you may not be worried about at this point.