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Thanks, @alchemage! Probiotics, especially from fermented food sources like sauerkraut, kimchi, and kombucha, are generally a wise addition to any healthful routine. Gut flora is super important to wellness, since most neurotransmitters are created there! The guts are super key to the health of the immune system as well. Do you have a source you'd be willing to share that states DE kills good microbes so we can do some more research?

There are many parasites that are microorganisms. Parasitic worms are not necessarily microscopic but are considered synonymous by epidemiologists.

I'm having a hard time finding peer reviewed studies about microorganisms and DE. However, on this website for DE it claims to kill bacteria as well as a long list of other benefits. [ https://diatomaceous.org/about/ ]

All in all, it doesn't seem that there have been many studies at all on DE and that much information is based upon anecdotal references.