S.B.
This is a question for the pediatrician.
Some antibiotics are to be taken with food. Some are to be taken an hour before. Some are to be taken with no dairy.
It all depends on the antibiotic and the most effective way for it to enter the system so it can do it's work.
I'm not against probiotics, but you need to make sure, any time your child is on an antibiotic, that you aren't countering with something that will render the antibiotic ineffective.
Your pediatrician needs to know everything your son commonly takes so they can advise how long in between or stopping one thing all together until the course of antibiotics is done.
I really would consult the pediatrician about it so that you have the correct and best answer.
Best wishes.