Why are bacteria referred to using botanic terms (flora, blooming)?

I've seen a lot of information lately about intestinal flora or gut flora but I was under the impression that flora refers exclusively to plant life. So how did bacteria come to be called flora? I am aware that they aren't really animals either, but naming them after plant life seems... wrong.

To confuse matters further, aquariums often suffer from a condition called bacterial blooming which has nothing to do with flowers.

P.S. There is indeed a Yahoo Answers! post about this topic, but it would be nice to have a more language-based discussion.

If you look at the entry for flora at dictionary.com you can see:

flora noun — 4. the aggregate of bacteria, fungi, and other microorganisms normally occurring on or in the bodies of humans and other animals: intestinal flora.

Furthermore, if you look at the entry at etymonline you can see this:

extended form of *bhel- (3) "to thrive, bloom,"

Which is talking about the PIE root. It seems appropriate to use flora to refer to fungi, bacteria, algae, etc., because they all bloom and *bhel- is the origin of the word bloom.

English speaking scientists will often take words from English, especially ones with a Latin or a Greek base, and use them for what seems appropriate at the time. Sometimes the scientific meaning comes back into the mainstream. E.g. orbit, torus, virus, etc.