I am currently running the parasites general comprehensive set and want to know if that would have a negative effect on the healthy strains in the gut?

When parasites are killed off they release all kinds of toxic material (viruses, pathogenic bacteria, fungi, mycotoxins), which can damage healthy bacteria in the gut. But some consider getting rid of a chronic infection like a parasite colony to be more important than a well balanced gut flora.

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http://www.spooky2.com/forums/viewtopic.php?f=12&t=5639