A good question. I can't see anything stupid about it.
The stupid thing is that "normal" language users (and especially foreign learners of Polish) can't analyse each word with the case-by-case method. It won't do any good, because there are too many words in Polish (or any language).
It's just a job for professional linguists who don't have more interestings things to do (/joke).Other stupid thing is that the original poster could have some research on ethymology by himself instead of asking us at the PFs.
BTW, it's not bacterium, the word (at least according to PWN Encyclopedia) comes from Greek:
bakterie [gr. bakterion ‘laseczka’]
And according to Wiki:
Bacteria were first observed by Antonie van Leeuwenhoek in 1676, using a single-lens microscope of his own design. He called them "animalcules" and published his observations in a series of letters to the Royal Society. The name bacterium was introduced much later, by Christian Gottfried Ehrenberg in 1838, and is derived from the Greek word - , bacterion -a , meaning "small staff"
This word didn't follow the normal evolution of Latin words borrowed by the Polish language, like gymnasium (also from Greek "gymnásion"), because it was implemented artificially at a certain point of time.
speakers unaware of its singular form started confusing the plural form with the singular one (Polish speakers often use Latin words and expressions incorrectly, so there's nothing surprizig about it). Such usage has become very widespread, so bacteria has become the singular form through the usage, and because it ends with "a", it is feminine.
I don't agree with that, I rather assume that:
1/ the word bacterium was first known to scientists, who were aware of the Latin forms (because the Latin was much needed for a scientist even a hundred years ago).
2/ in German: die Bakterie (feminine), pl. Bakterien
it was rather German language publications that were the main source of the knowledge about bacteria for Polish scientists, and they adapted the germanized feminie version, which sounds more natural to the Polish ear (because all those Latin words ending in -um/-ium aren't exactly easy in declension as the ending is untypical for the Polish language).