Man, I am now convinced the cipro/flagyl combination is what set the stage here. So….how did you find out you had an autoimmune condition? I have abnormal liver enzymes and a "severe" bacterial imbalance according to my functional doctor. I am awaiting the results of the SIBO breath test and todays unltrasound to get a game plan ready. The doc did mentioned a likely course of neomycin, bactrim, and then nystatin. That, along with dietary changes of course. I can relate to you on the fatigue part…..seems like I am walking through cement all day.