[teaearlgraycold]

Not quite what you asked, but I know of why another really common set of micro organisms wasn’t noticed. Megaviruses, which rival bacteria in size, were only discovered in the last couple of decades. They’re everywhere. But when people would look for viruses they’d do so specifically by sorting matter in samples by size. So effectively by definition a virus would have to be small. We’d been looking at them under microscopes for over a hundred years but assumed they were inert particles.