If I were reconstructing the entire biosphere, unless I had a really good reason, I’d leave out bacteria that made people stink, and especially endemic diseases like Cutibacterium acnes which are unavoidable today but didn’t always affect humans. There are good reasons to think that no one had acne until about 7000 years ago when people started cultivating grape vines and picked up something that lives on them, and that could be true after the apocalypse if Gaia didn’t choose to put the same thing on grapes.