Clean vs. dirty isn't even the right way to think about it. We used to be immersed in an environment full of life, and now we live in mostly sterile environments free of life except for maybe some of the first wave colonizer specialist microorganisms. You are filled and covered with life that isn't from your own genes, and that microbiome is now mostly disconnected from the biosphere.

I get some weird skin issues sometimes which are almost magically fixed if I visit a natural body of water... it's clearly an issue of my immune system interacting unfavorably with a microbiome which is out of whack.