As Lyme Disease creates systemic inflammation in the body. It can become difficult for the small glands in the body to function properly. This is true for the hypothalmus, pineal gland, the thyroid, adrenals, etc.
Some Lyme patients immune system gets so disregulated that auto immune thyroid conditions (Hashimoto's) can occur.
Helping the thyroid is of the utmost importance when healing from Lyme. Thyroid and adrenals are the horses that pull the buggy! If they are not working, you are not working.
Amy Meyers, MD explains the difference between thyroid meds and all the binders and additives in them. Those of you on Ketogenic diets, beware; some thyroid meds have starch binders in them.
Stop the Thyroid Madness explains about the connection between thyroid imbalance and Lyme
Dr. Nikolas Hedberg explains connection between Lyme and Hashimoto's.
He also has a video about thyroid and herbal medicine. If you are more of a reader than audio-visual person you can see the write up of that information here.