Killing 50% of your gut bacteria is a big nothing.

These things reproduce on the timescale of hours.

I kill 90% of my sourdough starter every time I feed it, and it bounces back the same day.

That would imply that 50 percent of the snapped people’s biomes remained behind. All of the produce in the grocery stores would be covered in an airborne mist of E. coli, and snapped surgeons that were mid-operation would give their patients staph infections, assuming the suriviving surgery team was able to stablize and close them up before they died anyway. Neat.

Also when those snapped people returned with the half of their biomes that also got snapped, you would get a sequel to the diarrhea. Diarrhea 2: Electric Boogapoo.

50% of all ≠ 50% per person