I was on Flagyl and azithromycin for over 4 months, and the results were great. I am hoping to go back on it soon. I felt
Stomach upset is the main drawback, but as said above, being careful to take it with 'cushioning' food takes care of that. I would use yogurt or bread, and would eat not with or after the meds, but before and with the meds -- 15 minutes or so beforehand just to give the ole stomach a warning.
I took florastor (which is a well-known brand of S. boulardii) at my dr's insistence, and you should too. One capsule twice a day for me. I took each one with the 'pre-dose' of food (bread, yogurt) so the capsules could deploy, but I know someone who takes the meds and the probiotic all at once with no problem -- stronger stomach than mine, which is touchy.
My husband had to take this recently for an infection he received after surgery. The only problem he had was nausea. Usually eating something with the pill works. You may want to consider probiotics after you are off it.
I posted a few weeks ago asking the same question. I will start it in two weeks along with Ceftin. LLMD said I would be taking it for two weeks and off two weeks. Some said that it was great in reducing the brain fog. There can be some stomach discomfort. Liver needs to be monitored. Here is the link to the question I posted.
http://www.medhelp.org/posts/Lyme-Disease/Flagyl/show/797156?personal_page_id=408084&post_id=post_4233477