Hi LymeUnkown. The best kind of acidophilus to get are those that are refrigerated and that have a high culture count (such as 9 billion cultures per capsule). Most health food stores have them. These need to be taken at least two hours apart from the antibiotics or they will not be effective.
I am sorry your father is not well. If you feel something else is going on, why not switch doctors to see if another one can help?