I Have Been Taking Doxycycline For 2 Months Now Following

I have been taking Doxycycline for 2 months now following a tic bite carrying Lyme infection. How long should I continue the treatment? I have some IBS distress from the medicine but nothing severe. I was told 3 months of this medicine should hopefully prevent the Lyme infection from spreading through my system. But the side effects also concern me. I do feel flu like symptoms and my IBS is worse but I think Lyme disease is a greater risk. Are my symptoms common for someone on this medication?