The yogurt should be helpful, but if you are taking a good probiotic, you might want to skip the yogurt as well. I'm just learning about Lyme, but I previously had chronic sinusitis, and was on anibiotics for what I thought was a long duration at the time, and on and off all my life (nothing compared to this). I went on a yeast free diet, which excluded dairy. Also if there is sugar added to the yogurt, it could feed the yeast, which would cancel out the benefit. I did eat almonds and even almond butter, but avoided peanuts. You may be sensitive to the almonds though.
I'm still trying to figure out what dietary changes to make, but am thinking that I need to do the full yeast free diet, since I don't know how long I will be on the Doxycycline this time, or if the dose will even be increased once I get to the ID specialist. It's hard, but worth it to feel better.