Vincent, are you waiting at least two hours before or after taking the antibiotic to take the acidophilus? If you do not wait two hours, the antibiotic will not be absorbed properly.
A couple of other tips that you may already know: Do not eat dairy products two hours before or after taking it, or it will not be absorbed properly. Is this why the doctor told you not to have calcium?
When on Doxy, stay out of the sun. You can get a severe sunburn in just a few minutes, even with sunscreen on. Also, do not lay down for at least an hour after taking the Doxy or you could ulcerate your esophagus (this should be listed on the pharmacy sheet). This happened to me and it is extremely painful. If it makes you nauseous, eat something substantial and non-dairy when taking it.