I agree - you have just confirmed for yourself that it is time to begin a complementary program to boost immunity. You can do that in conjunction with your doctors' treatment - and hopefully you just won't end up calling him much anymore...! ( I just can't understand the nurses reasoning. Enzymes don't work in the wrong Ph, and soothing the GI will most certainly help weight gain and possibly coughing...)

I would still push for a stool test, Maybe doctor's data will take a prescription for a test kit and then the rest is up to you (doing the test, sending it in, paying). The results will guide you.

The probiotics can be started right away.

Consider the depletion caused by antacids if prescribed --or anything else. http://www.spectracell.com/research/pdf/DrugDepletions.pdf

Just FYI about an interesting site -- http://www.cysticus.de/english/index.htm
lots of holistic ideas