A possible choice for a "medical-grade" probiotic is VSL#3. The capsules (I would not recommend the sachets due to fillers) have 250 billion beneficial bacteria. As with most things here, not everyone has good success with VSL, while others swear by it. My local Walgreens has ordered it in for me in the past.
You might want to consider making your own yogurt because it has 4 times the beneficial bacteria that store-bought yogurt has. The book "Nourishing Traditions" by Sally Fallon also explains how to make other fermented foods for their beneficial bacteria, such as sauerkraut and fruit chutneys.
Yes, take the probiotics while on antibiotics. Experts say to take them two hours before or after your antibiotic to lessen the killing of beneficial bacteria by the anti's.
Lastly, if you are going the cipro+flagyl route, you might want to consider what AyurvedaHeals said and take a probiotic with Saccharomyces boulardii. Florastor is a name brand that doctors often prescribe, but I'm sure there are others. S. boulardii has been proven to fight/prevent C diff. infections which are sometimes caused by the big-gun antibiotics. Here's what Wiki says:
Good luck to you!
Mom to 17 year old son diagnosed in June, 2007.
Omega 3s, digestive enzymes, probiotics, vit. C, calcium, vit. D3, a good multivitamin and SCD legal yogurt
Started The Maker's Diet in Sept. '07. Incorporate Specific Carbohydrate Diet (SCD) recipes, too. Med-free.http://www.healingwell.com/community/default.aspx?f=17&m=984588http://www.healingwell.com/community/default.aspx?f=17&m=1533705http://www.healingwell.com/community/default.aspx?f=17&p=1&m=1262312