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Thanos' snap wouldn't kill 50% of each survivors' gut microbiome, it would kill 50% of all the lil buggies that compromise all gut microbiomes, and if the snap effects individuals randomly, you'd see a normal distribution (I think, I haven't taken stats in a decade). So some survivors would retain 100% of their microbiome, some would lose it all, with a bell curve in between, probably with the peak around 50%.
That bell curve would be extremely narrow. You have so many lil buggies that basically every human survivor would lose ~50% buggies.
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