I suggest you read some on CZ or net about the bacteria overgrowth they discovered E.coli and the other stuff. They do like acidic environment but this could be created by something else...Like parasites or yeast
Maybe research on non acidic creating probiotics and also in the same time decrease ecoli enterobacter numbers. I would focus on gut first the other problems seem secondary.
You could try mashed garlic with each meal and probiotics after? avoid fermentable food these bacteria like starch and stuff. And maybe use mild antibacterial herbs. Possible sauerkraut not ok cause have high acid bacteria. Maybe s.boulardii search the net for forums.
Btw what lab did you use cause seems like a good job they done? Language seems like Dutch or something