Wryter, make sure you take a good probiotic with any treatment. One of the better ones is Therbiotic complete by Klaire Labs though there are many good choices.
Some other natural antibiotic supplements out there that would be good in a Lyme protocol are p73 super strength oil of oregano by North American Herb and Spice and grapefruit seed extract (like WWJD mentioned) which is supposed to act as a natural cyst-buster.
Good luck and keep us informed of your progress.