Re: Which antifungals have least effect on beneficial bacteria.

I agree: GSE, Garlic, and Oregano Oil will kill-off your friendly flora.

Caprylic acid destroys some beneficial bacteria (maybe around 50%), but it is probably one of the "optimal" anti-fungals in terms of balancing your gut flora. Caprylic acid is in mother's milk ... so that provides strong evidence as to nature's view of its importance. Undecylenic acid is another similar anti-fungal, but I don't know its affect on gut flora.