In theory, according to the Borody protocol, both you and your donor are supposed to get a battery of tests which would typically not be covered by insurance (they were not on ours) and cost a fortune. I got my wife to be my donor and I barely tested myself for any of them items (seeing as I am not exactly going to infect myself), but even though it seems a bit silly to be testing a spouse with which one is already sharing every germ, I had her tested for about
80% of the items listed, and it cost around $1500 for all those blood tests (ouch!!). She came out pretty clean- though some items are ambiguous grey areas because most of the healthy population will show antibodies indicative of exposure to something or another over the course of their life.
In the end, I discontinued the HPI after the second day, because it immediately resulted in a flareup for me that seemed pretty clearcut cause-effect. I haven't whipped up the courage since to try HPI with another donor though I sometimes consider travelling and using a sibling as my donor- but the cost of those tests was so insane that I am reluctant to go to the trouble again. My wife's stool may just not have been the greatest mix of probiotics- her stools tend to be soft and mushy although she does not have any diagnosed intestinal ailments.