Long-term antibiotic use can severely damage gut microbiome diversity, making repopulation with beneficial bacteria extremely difficult.

“Well, maybe you just completely scorched earth your microbiome among other things. So one of my theories is that what people perceive as chronic Lyme is in fact a collection of similar symptoms caused by the long course of antibiotics. So you should focus on prebiotics, probiotics. I have had a tremendous amount of difficulty, at least as measured in common stool testing and so on, in repopulating my gut diversity. It's been extremely hard.”