Misleading title. Article is about how microbes fit into evolutionary theory. Evolution itself does not change the way it "treats" anything. It is what it is, what changes is what WE, as humans, think is going on.
We evolved with microbiome. Viruses were part of us during our evolutionary journey, no?
I think that's the GP's point: microbes are subject to the evolutionary pressures that affect their host
Yeah, the title reads as if there's some sort of moral imperative evolution ought to be following.