Now, if there comes a point and time (and these will become few and far between once you start working with your Naturopathic Doctor) where you just need to take an antibiotic, you MUST also take probiotics.
Now this is where the confusion comes in. Since antibiotics work by killing off bacteria many assume that taking probiotics is a waste since they'll just be wiped out by the antibiotics. This is not true!
I'm going to borrow an analogy from Dr. Jason Hawrelak, a practicing ND who does extensive research into the area of probiotics. Think of your digestive tract as a parking lot. Occupying each parking space is beneficial bacteria. We want to have each space occupied with the good bacteria so that no space is left open for the pathogenic "bad" bacteria to park. With each dose of the antibiotic, some good bacteria is wiped out from their space. We want to make sure to continuously re-fill these spaces with the good probiotics so we can keep the parking lot full.
Research continuously shows that probiotics given during the course of antibiotics reduces antibiotic related side effects (think digestive upset and yeast infections to name a couple) and reduces the damage done to the balance of gut bacteria. The benefit of giving probiotics alongside antibiotics is far superior than giving probiotics after the course of antibiotics is finished.
Probiotics should be taken along with antibiotics, but the timing should be separated as much as possible. That is, take the probiotic as far away as possible from the antibiotic.
Keep in mind that not all probiotics are created equal. Be sure to purchase a quality probiotic from your Naturopathic Doctor or from a reputable company that is ensuring the appropriate strain in the appropriate amount is present.