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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.

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Bacteria are neither plants nor animals. Come to that, fungi and algae aren't plants either, but I bet you don't think there's anything odd about lumping them in with flora. I just think of flora as everything alive that's not fauna. It's just that the more noticeable flora are plants, and most of us get a bit vague when it comes to classifying, say, yeast or viruses. – FumbleFingers Nov 12 '11 at 4:29
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They aren't named after plants. I think the problem is that your impression is that flora means plants. Once you get around that problem it is a lot clearer:-) – Rory Alsop Nov 12 '11 at 10:08
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Gasp! You mean Wikipedia is wrong? – saritonin Nov 12 '11 at 14:05

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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.

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