As far as I recall, Dr. Clark says not to take the probiotics because they also contain harmful strains of bacteria. She also says of zapping and bowel bacteria-killing herbs like turmeric, fennel, oregano oil, that the bowel will recolonize itself in 1-2 days anyway so the probiotics are not necessary.
But I do remember her recommending Raw Milk for Lactoferrin in the Advanced Cancer Book (sterilized first) so if this is a concern, the raw milk or homemade raw milk yogurt could maybe be used. It is strange that not much is said of yeast and fungus, esp. systemic, in her books. In the most recent info I've seen from her on cancer I see that new parasite measures are used for an extended time with Oregano Oil being used for 6 months (which may be to kill off fungus?). It also states that our bodies are overrun with bread yeasts and funguses. I'm hoping her new book will come out soon and address this more, fungus is such a problem for so many of us!
If you're interested, I think I saw the above newer cancer info on drhuldaclark.org.