About your dysbiosis...I thought I had this too until I ran the giardia and salmonella scripts, and then adenovirus for good measure. It worked wonders on my digestion. I haven't run the shigella but that one's also important.
If you want to add good bacteria use Re-Flora by Vaxa. It's the best probiotic product I've ever tried, and I've spent a lot of money of probiotics over the years.