Hi Carrie.
I really don't know much about much but this is one area I have studied seriously for several years. First of all, recent studies at the University of Michigan show that after a one week treatment of antibiotics the gut flora is so drastically changed in mice (and people) that the immune systems are tilted to the bad Th2 immune response. Healthy cfers experience a Th1 response. Those same researchers call the current problem with with antibiotics and associated allergies, asthma and lung disorders the "hygiene hypothesis" It has been proven through research that after one dose of antibiotics gut flora is so changed that upon introduction of molds such as aspergillus, the subjects immediately developed allergic sensitivity proven by inflammatory markers in blood and tissue. These same subjects had no allergic response to molds before antibiotic usage.

At the most renowned respiratory hospital in the country (National Jewish in Denver), patients undergoing long term antibiotic treatment (chemotherapy) are urged to take probiotics 3 times a day. I know this because I am a patient there. The only advice is to take it 2 hours after antibiotics.

Also, other research shows in mice (but as you know CFTR knockout mice very much resemble in vivo CF) when administered acidophilus and L.Casei before pseudomonas challenge, the mice did not get pseudomonas. On the other hand, the mice who did not get probiotic dosage before challenged with pseudo became infected with the pathogen.

Also, keep in mind that certain probiotics are associated with dfferent immune response. For example, L. acidophilus induces chemicals in the body that support Th1 response. I have read conflicting info on S. Thermophilus (this is the one in most traditional yogurts) Most of the research I have found suggests it induces a more Th2 response (the one we don't want) Th2 immune response is responsible for allergies and inflammation without purspose. Th1 response is our fighting response!!!

I can send you all of these studies if you like and can go into much more detail.
mandy